From 2ee0f753ef638bec0e585f4bbfd2a31f849f43f4 Mon Sep 17 00:00:00 2001
From: jasonjgill <43014222+jasonjgill@users.noreply.github.com>
Date: Fri, 30 Aug 2024 11:23:46 -0500
Subject: [PATCH 1/6] Update cpt.yaml

Add 5 tools, remove 2 tools
---
 cpt.yaml | 28 ++++++++++++++++++++--------
 1 file changed, 20 insertions(+), 8 deletions(-)

diff --git a/cpt.yaml b/cpt.yaml
index e508053b..8693ff68 100644
--- a/cpt.yaml
+++ b/cpt.yaml
@@ -64,18 +64,10 @@ tools:
     owner: cpt
     tool_panel_section_label: Annotation
 
-  - name: cpt_intersect_adjacent
-    owner: cpt
-    tool_panel_section_label: Annotation
-
   - name: cpt_related_genomes_nuc
     owner: cpt
     tool_panel_section_label: Phylogenetics
 
-  - name: cpt_related_genomes_prot
-    owner: cpt
-    tool_panel_section_label: Phylogenetics
-
   - name: cpt_xmfa_to_table
     owner: cpt
     tool_panel_section_label: Phylogenetics
@@ -127,3 +119,23 @@ tools:
   - name: cpt_fasta_translate
     owner: cpt
     tool_panel_section_label: Annotation
+    
+  - name: cpt_protein_blast_grouping
+    owner: cpt
+    tool_panel_section_label: Annotation
+
+  - name: cpt_prophage_relatedness
+    owner: cpt
+    tool_panel_section_label: Annotation
+
+  - name: cpt_intersect_adj
+    owner: cpt
+    tool_panel_section_label: Annotation
+
+  - name: phageterm
+    owner: mmonot
+    tool_panel_section_label: Annotation
+
+  - name: phagetermvirome
+    owner: bioit_sciensano
+    tool_panel_section_label: Annotation

From 64a26f98a1ff0876e4dc37cf5f93bfecf1a6ac9d Mon Sep 17 00:00:00 2001
From: jasonjgill <43014222+jasonjgill@users.noreply.github.com>
Date: Fri, 30 Aug 2024 11:29:01 -0500
Subject: [PATCH 2/6] Update cpt.yaml

added defense_finder
---
 cpt.yaml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/cpt.yaml b/cpt.yaml
index 8693ff68..e80a0872 100644
--- a/cpt.yaml
+++ b/cpt.yaml
@@ -139,3 +139,7 @@ tools:
   - name: phagetermvirome
     owner: bioit_sciensano
     tool_panel_section_label: Annotation
+    
+  - name: defense_finder
+    owner: rplanel
+    tool_panel_section_label: Annotation

From e73c9853a55ec5bdbbe682a7b69201a2033a5bc4 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-bot@github.com>
Date: Sat, 31 Aug 2024 23:25:54 +0000
Subject: [PATCH 3/6] Updated trusted tools (2024-08-31)

---
 cpt.yaml.lock               | 40 +++++++++++++++++++++++++++----------
 genome-annotation.yaml.lock |  1 +
 tools_iuc.yaml.lock         |  7 +++++++
 3 files changed, 38 insertions(+), 10 deletions(-)

diff --git a/cpt.yaml.lock b/cpt.yaml.lock
index 5b9e4320..a3a7a666 100644
--- a/cpt.yaml.lock
+++ b/cpt.yaml.lock
@@ -91,21 +91,11 @@ tools:
   - 2654bcd9b14d
   - b79df4966ebb
   tool_panel_section_label: Annotation
-- name: cpt_intersect_adjacent
-  owner: cpt
-  revisions:
-  - 7e393668b4b9
-  tool_panel_section_label: Annotation
 - name: cpt_related_genomes_nuc
   owner: cpt
   revisions:
   - 5a5fe0a6f78d
   tool_panel_section_label: Phylogenetics
-- name: cpt_related_genomes_prot
-  owner: cpt
-  revisions:
-  - ebcc87a27f9c
-  tool_panel_section_label: Phylogenetics
 - name: cpt_xmfa_to_table
   owner: cpt
   revisions:
@@ -182,3 +172,33 @@ tools:
   revisions:
   - cb42bee49abb
   tool_panel_section_label: Annotation
+- name: cpt_protein_blast_grouping
+  owner: cpt
+  revisions:
+  - 11701cc63084
+  tool_panel_section_label: Annotation
+- name: cpt_prophage_relatedness
+  owner: cpt
+  revisions:
+  - 7ba8b1f0fdf0
+  tool_panel_section_label: Annotation
+- name: cpt_intersect_adj
+  owner: cpt
+  revisions:
+  - 00aab5199327
+  tool_panel_section_label: Annotation
+- name: phageterm
+  owner: mmonot
+  revisions:
+  - 26ceb3225190
+  tool_panel_section_label: Annotation
+- name: phagetermvirome
+  owner: bioit_sciensano
+  revisions:
+  - ee73cdf35532
+  tool_panel_section_label: Annotation
+- name: defense_finder
+  owner: rplanel
+  revisions:
+  - 4ff81ce331f9
+  tool_panel_section_label: Annotation
diff --git a/genome-annotation.yaml.lock b/genome-annotation.yaml.lock
index eba9d05c..4f78f926 100644
--- a/genome-annotation.yaml.lock
+++ b/genome-annotation.yaml.lock
@@ -103,6 +103,7 @@ tools:
   - 1440ae06552f
   - 1e62c28ba91d
   - 2a5b8b9936bf
+  - 2babe6d5c561
   - 2dd755c1c6ff
   - 4048d82f0c88
   - 41030a6c03b7
diff --git a/tools_iuc.yaml.lock b/tools_iuc.yaml.lock
index 6ccba5b3..5c5fb9e1 100644
--- a/tools_iuc.yaml.lock
+++ b/tools_iuc.yaml.lock
@@ -61,6 +61,7 @@ tools:
   revisions:
   - 0d243f458b53
   - 2a5b8b9936bf
+  - 2babe6d5c561
   - 2dd755c1c6ff
   - 41030a6c03b7
   - 46ae58b1d792
@@ -1169,6 +1170,7 @@ tools:
   - 8e66f695d859
   - 96f74538896e
   - e989670c7fc7
+  - f73ab5187eed
   - f89e3c318453
   tool_panel_section_label: Assembly
 - name: rnaspades
@@ -4025,18 +4027,21 @@ tools:
 - name: cami_amber
   owner: iuc
   revisions:
+  - 9ed513717fc4
   - afc795d10918
   - f801b844f239
   tool_panel_section_label: Metagenomic Analysis
 - name: cami_amber_add
   owner: iuc
   revisions:
+  - 2e6ddf48a213
   - 433fb72344cb
   - b07cfe3b877e
   tool_panel_section_label: Metagenomic Analysis
 - name: cami_amber_convert
   owner: iuc
   revisions:
+  - 848594e0be6a
   - 8754ed6f0096
   - 8f0e53330d8e
   tool_panel_section_label: Metagenomic Analysis
@@ -4054,6 +4059,7 @@ tools:
   owner: iuc
   revisions:
   - 1e10251b9615
+  - d368e312aebd
   tool_panel_section_label: Metagenomic Analysis
 - name: krakentools_kreport2krona
   owner: iuc
@@ -8900,6 +8906,7 @@ tools:
   - 8e66f695d859
   - 96f74538896e
   - e989670c7fc7
+  - f73ab5187eed
   - f89e3c318453
   tool_panel_section_label: Assembly
 - name: rseqc

From 7510dedb58ce098f9a4add659463ea6ffc921df4 Mon Sep 17 00:00:00 2001
From: jasonjgill <43014222+jasonjgill@users.noreply.github.com>
Date: Fri, 6 Sep 2024 16:06:00 -0500
Subject: [PATCH 4/6] Update cpt.yaml

Added back cpt_intersect_adjacent and cpt_related_genomes_prot for repeatability issues with comments, removed phageterm, phagetermvirome and defense_finder, will deal with these in a future PR. Net change is adding 3 new CPT tools.
---
 cpt.yaml | 21 ++++++++++-----------
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/cpt.yaml b/cpt.yaml
index e80a0872..3d0ecd1a 100644
--- a/cpt.yaml
+++ b/cpt.yaml
@@ -63,11 +63,21 @@ tools:
   - name: cpt_lipory
     owner: cpt
     tool_panel_section_label: Annotation
+    
+  - name: cpt_intersect_adjacent
+    owner: cpt
+    tool_panel_section_label: Annotation
+## deprecated tool, replaced by cpt_intersect_adj
 
   - name: cpt_related_genomes_nuc
     owner: cpt
     tool_panel_section_label: Phylogenetics
 
+  - name: cpt_related_genomes_prot
+    owner: cpt
+    tool_panel_section_label: Phylogenetics
+## deprecated tool, replaced by cpt_protein_blast_grouping
+
   - name: cpt_xmfa_to_table
     owner: cpt
     tool_panel_section_label: Phylogenetics
@@ -132,14 +142,3 @@ tools:
     owner: cpt
     tool_panel_section_label: Annotation
 
-  - name: phageterm
-    owner: mmonot
-    tool_panel_section_label: Annotation
-
-  - name: phagetermvirome
-    owner: bioit_sciensano
-    tool_panel_section_label: Annotation
-    
-  - name: defense_finder
-    owner: rplanel
-    tool_panel_section_label: Annotation

From fadd0b3f55b22aa0887bbe6a4fbad3c42c2945a1 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-bot@github.com>
Date: Sat, 7 Sep 2024 23:26:25 +0000
Subject: [PATCH 5/6] Updated trusted tools (2024-09-07)

---
 asaim.yaml.lock         |  1 +
 bgruening.yaml.lock     |  2 ++
 cpt.yaml.lock           | 25 ++++++++++---------------
 ecology.yaml.lock       |  2 ++
 europe-custom.yaml.lock |  2 ++
 tools_galaxyp.yaml.lock |  1 +
 tools_iuc.yaml.lock     | 25 +++++++++++++++++++++++++
 7 files changed, 43 insertions(+), 15 deletions(-)

diff --git a/asaim.yaml.lock b/asaim.yaml.lock
index 8dfd609a..e84522ba 100644
--- a/asaim.yaml.lock
+++ b/asaim.yaml.lock
@@ -85,6 +85,7 @@ tools:
   - c19b16e5729c
   - e4574a4d09d8
   - f7985e0479b9
+  - f7e2f1eb3a16
   tool_panel_section_label: Quality Control
 - name: format_cd_hit_output
   owner: bebatut
diff --git a/bgruening.yaml.lock b/bgruening.yaml.lock
index 82797b8b..88281dd9 100644
--- a/bgruening.yaml.lock
+++ b/bgruening.yaml.lock
@@ -262,6 +262,7 @@ tools:
   - b1260bca5fdc
   - b55199c56abd
   - c017111e976a
+  - c4b77883c0a7
   - dc3fe98e7b37
   tool_panel_section_label: Graph/Display Data
 - name: plotly_ml_performance_plots
@@ -289,6 +290,7 @@ tools:
 - name: bioimage_inference
   owner: bgruening
   revisions:
+  - b0f2d3b4a278
   - caea9ee1ffac
   tool_panel_section_label: Imaging
 - name: woundhealing_scratch_assay
diff --git a/cpt.yaml.lock b/cpt.yaml.lock
index a3a7a666..645d2052 100644
--- a/cpt.yaml.lock
+++ b/cpt.yaml.lock
@@ -91,11 +91,21 @@ tools:
   - 2654bcd9b14d
   - b79df4966ebb
   tool_panel_section_label: Annotation
+- name: cpt_intersect_adjacent
+  owner: cpt
+  revisions:
+  - 7e393668b4b9
+  tool_panel_section_label: Annotation
 - name: cpt_related_genomes_nuc
   owner: cpt
   revisions:
   - 5a5fe0a6f78d
   tool_panel_section_label: Phylogenetics
+- name: cpt_related_genomes_prot
+  owner: cpt
+  revisions:
+  - ebcc87a27f9c
+  tool_panel_section_label: Phylogenetics
 - name: cpt_xmfa_to_table
   owner: cpt
   revisions:
@@ -187,18 +197,3 @@ tools:
   revisions:
   - 00aab5199327
   tool_panel_section_label: Annotation
-- name: phageterm
-  owner: mmonot
-  revisions:
-  - 26ceb3225190
-  tool_panel_section_label: Annotation
-- name: phagetermvirome
-  owner: bioit_sciensano
-  revisions:
-  - ee73cdf35532
-  tool_panel_section_label: Annotation
-- name: defense_finder
-  owner: rplanel
-  revisions:
-  - 4ff81ce331f9
-  tool_panel_section_label: Annotation
diff --git a/ecology.yaml.lock b/ecology.yaml.lock
index 52fa5389..a56532a2 100644
--- a/ecology.yaml.lock
+++ b/ecology.yaml.lock
@@ -912,6 +912,7 @@ tools:
   - bf675f34b056
   - c19b16e5729c
   - f7985e0479b9
+  - f7e2f1eb3a16
   tool_panel_section_label: Quality Control
 - name: mothur_sffinfo
   owner: iuc
@@ -1653,6 +1654,7 @@ tools:
 - name: hirondelle_crim
   owner: ecology
   revisions:
+  - 52baddd15640
   - afede0916f0a
   tool_panel_section_label: GIS Data Handling
 - name: aquainfra_importer
diff --git a/europe-custom.yaml.lock b/europe-custom.yaml.lock
index 6c486cea..ce80dde4 100644
--- a/europe-custom.yaml.lock
+++ b/europe-custom.yaml.lock
@@ -884,6 +884,7 @@ tools:
   - 2f804526f5fd
   - 581e52f03c5d
   - b4c6f054210a
+  - f69501361cec
   tool_panel_section_label: FASTA/FASTQ
 - name: fastx_artifacts_filter
   owner: devteam
@@ -1080,6 +1081,7 @@ tools:
   - bf675f34b056
   - c19b16e5729c
   - f7985e0479b9
+  - f7e2f1eb3a16
   tool_panel_section_label: Quality Control
 - name: mira_assembler
   owner: peterjc
diff --git a/tools_galaxyp.yaml.lock b/tools_galaxyp.yaml.lock
index 1ea5b65d..14dfe471 100644
--- a/tools_galaxyp.yaml.lock
+++ b/tools_galaxyp.yaml.lock
@@ -561,6 +561,7 @@ tools:
   - 064b53fd3131
   - 17c54a716a5b
   - 24ccdcfbabac
+  - 6a8cf86fd3b7
   - 7bee859bbd11
   - 9f136ebf73ac
   - b5e9cebb27e3
diff --git a/tools_iuc.yaml.lock b/tools_iuc.yaml.lock
index 5c5fb9e1..e2265318 100644
--- a/tools_iuc.yaml.lock
+++ b/tools_iuc.yaml.lock
@@ -53,6 +53,7 @@ tools:
   - 865ece5ca178
   - 92eee5f31117
   - ba6990f72184
+  - d77802fe76f7
   - da5f1924bb2e
   - debdc1469b41
   tool_panel_section_label: Annotation
@@ -1481,6 +1482,7 @@ tools:
   - 27673f5b5343
   - 359e043a285c
   - 405ed9ad53ab
+  - 767943cd85bf
   - 7ecb45126cd2
   - a68cb16fa1a0
   - b226e0c805a5
@@ -1538,12 +1540,14 @@ tools:
   - 158b5b2a164a
   - 5051467dc96a
   - 60ca8d013263
+  - 6ee334657360
   - e13f565068d6
   - e5340c09200a
   tool_panel_section_label: Convert Formats
 - name: crossmap_bed
   owner: iuc
   revisions:
+  - 50b7875a49d0
   - 91efc13d3ec1
   - cdbdce00f5f6
   - e6c68525e9ee
@@ -1556,6 +1560,7 @@ tools:
   - 09c6a9e067f9
   - 42b239a32349
   - 4d97434ea0fb
+  - 75a08e10cc76
   - 88d180fb6d67
   - e80720e27001
   tool_panel_section_label: Convert Formats
@@ -1563,6 +1568,7 @@ tools:
   owner: iuc
   revisions:
   - 8635b6b8a8f2
+  - a50ef4d58c90
   - eb66d7a04bf8
   tool_panel_section_label: Convert Formats
 - name: crossmap_vcf
@@ -1574,6 +1580,7 @@ tools:
   - 97979c3d179f
   - 9d61d74f03a4
   - b21851ddcc79
+  - d4965adac10c
   tool_panel_section_label: Convert Formats
 - name: crossmap_wig
   owner: iuc
@@ -1583,6 +1590,7 @@ tools:
   - 5f893ed3c5ed
   - e72c320c17c1
   - e8d84292e510
+  - f7229c8445da
   tool_panel_section_label: Convert Formats
 - name: genebed_maf_to_fasta
   owner: iuc
@@ -2290,6 +2298,7 @@ tools:
   - 2f804526f5fd
   - 581e52f03c5d
   - b4c6f054210a
+  - f69501361cec
   tool_panel_section_label: FASTA/FASTQ
 - name: rcorrector
   owner: iuc
@@ -3828,6 +3837,7 @@ tools:
   revisions:
   - 09dbbf5d3201
   - 396cc0c65700
+  - 4ad7321205c9
   - 8a7462c0ac14
   - a07a2d9ddd42
   - a287431cdf4f
@@ -4390,10 +4400,12 @@ tools:
   revisions:
   - 5ee29434330f
   - 7ccea589e8b7
+  - bcb8dc01f296
   tool_panel_section_label: Metagenomic Analysis
 - name: checkm_lineage_set
   owner: iuc
   revisions:
+  - 3693acdbf0d6
   - 640400ad260d
   - b39999cdbf21
   tool_panel_section_label: Metagenomic Analysis
@@ -4401,29 +4413,34 @@ tools:
   owner: iuc
   revisions:
   - 760dc0c0e689
+  - 8345d273ba82
   - f0107b9f2dc3
   tool_panel_section_label: Metagenomic Analysis
 - name: checkm_plot
   owner: iuc
   revisions:
   - 356839cd89d2
+  - 9916308301da
   - b24e4f6c8b4d
   tool_panel_section_label: Metagenomic Analysis
 - name: checkm_qa
   owner: iuc
   revisions:
+  - 5466420816b9
   - 5c0493cdced9
   - 8236b90ce44c
   tool_panel_section_label: Metagenomic Analysis
 - name: checkm_taxon_set
   owner: iuc
   revisions:
+  - 407e50329077
   - 600b129adb72
   - e3f1c47246fd
   tool_panel_section_label: Metagenomic Analysis
 - name: checkm_taxonomy_wf
   owner: iuc
   revisions:
+  - 19e4e2d98ebb
   - 2e995a9aa00e
   - 91230b9141c1
   tool_panel_section_label: Metagenomic Analysis
@@ -4432,16 +4449,19 @@ tools:
   revisions:
   - 878d742dacf0
   - bb3b50fa4956
+  - d0d9e52a46b8
   tool_panel_section_label: Metagenomic Analysis
 - name: checkm_tree
   owner: iuc
   revisions:
   - 6d1c282e2ce2
   - 9b2790bca5b5
+  - ce3fd529a6ec
   tool_panel_section_label: Metagenomic Analysis
 - name: checkm_tree_qa
   owner: iuc
   revisions:
+  - 36ea6d5441c3
   - b9a38ce53252
   - dd51f61c2309
   tool_panel_section_label: Metagenomic Analysis
@@ -8322,6 +8342,7 @@ tools:
   - df99138d2776
   - e4574a4d09d8
   - f7985e0479b9
+  - f7e2f1eb3a16
   tool_panel_section_label: Quality Control
 - name: bayescan
   owner: iuc
@@ -8722,6 +8743,7 @@ tools:
   - 6e53e565fc6a
   - 9bdff28ae1b1
   - a8305cf0c951
+  - ae2aad0a6d50
   - d79ed3ec25fe
   - df0c8d0a5992
   - f2843df56434
@@ -11109,6 +11131,7 @@ tools:
   - 27fd1c1f00a8
   - 7303183cdb87
   - b43df0ce6c87
+  - e43f513583ee
   - fdbd97ff825e
   - ff0a8cda0c0b
   tool_panel_section_label: Variant Calling
@@ -11978,6 +12001,7 @@ tools:
   revisions:
   - 10232d2b5062
   - 2814c058a087
+  - e7b39a7e0024
 - name: deeptools_alignmentsieve
   owner: bgruening
   revisions:
@@ -12289,5 +12313,6 @@ tools:
   owner: iuc
   revisions:
   - 3cb0128a59a6
+  - 5147f08d67c9
   - ea6ea4029c47
   tool_panel_section_label: Metabolomics

From b5ddd754e2f12ae61d79fa9206def19574f82035 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-bot@github.com>
Date: Sat, 14 Sep 2024 23:37:01 +0000
Subject: [PATCH 6/6] Updated trusted tools (2024-09-14)

---
 bgruening.yaml.lock     |  1 +
 ecology.yaml.lock       | 15 ++++++++++++++
 eirene.yaml.lock        |  8 ++++++++
 tools_galaxyp.yaml.lock |  1 +
 tools_iuc.yaml.lock     | 43 +++++++++++++++++++++++++++++++++++++++++
 5 files changed, 68 insertions(+)

diff --git a/bgruening.yaml.lock b/bgruening.yaml.lock
index 88281dd9..5566d232 100644
--- a/bgruening.yaml.lock
+++ b/bgruening.yaml.lock
@@ -1027,6 +1027,7 @@ tools:
   owner: bgruening
   revisions:
   - 08c658e9aa9e
+  - 7770a4bd42e2
   - dab494dce303
   tool_panel_section_label: Machine Learning
 - name: graphmap_align
diff --git a/ecology.yaml.lock b/ecology.yaml.lock
index a56532a2..a290b54e 100644
--- a/ecology.yaml.lock
+++ b/ecology.yaml.lock
@@ -1510,6 +1510,7 @@ tools:
   owner: ecology
   revisions:
   - 3b0fa963ae3e
+  - 67b2cd9c2954
   - d4f168043757
   - debfa8a223c0
   tool_panel_section_label: Data and Metadata Management
@@ -1519,11 +1520,13 @@ tools:
   - 32707c9f5261
   - 6de4b4f70b7b
   - 8631291a1527
+  - c223db6625c1
   tool_panel_section_label: Data and Metadata Management
 - name: raster_template
   owner: ecology
   revisions:
   - 06e29cdc08bf
+  - 9eaf84bf856f
   - b34c5a70b706
   tool_panel_section_label: Data and Metadata Management
 - name: vector_template
@@ -1531,10 +1534,12 @@ tools:
   revisions:
   - 330f15f2ad3f
   - 559744b4c50c
+  - c65dd54f9807
   tool_panel_section_label: Data and Metadata Management
 - name: entities_template
   owner: ecology
   revisions:
+  - 1b11e38718af
   - 5bfceb4ef59b
   - 8de58d879d6e
   tool_panel_section_label: Data and Metadata Management
@@ -1544,11 +1549,13 @@ tools:
   - 0fe3b8bd9d8b
   - 4f5816b57c13
   - a5f887cfcf94
+  - d53b708cb348
   tool_panel_section_label: Data and Metadata Management
 - name: taxo_cov_template
   owner: ecology
   revisions:
   - 0cfc9b6da2ac
+  - 20224597fa2c
   - 2af7401f13e0
   - 9507334a3303
   - a45fa46f8010
@@ -1557,6 +1564,7 @@ tools:
   owner: ecology
   revisions:
   - 34dcb86a9351
+  - 4cf24a95c4ff
   - 59349973537f
   - 642e31c435c9
   - 8a697f446051
@@ -1571,16 +1579,19 @@ tools:
   - 3d14d6a4ef7c
   - 409d9329d2be
   - 5c0290c4225a
+  - 6fc2341a92cb
   - bd8b3e7541d5
   tool_panel_section_label: Data and Metadata Management
 - name: ecoregion_geonearestneighbor
   owner: ecology
   revisions:
+  - 36637718c51d
   - 5cde56683579
   tool_panel_section_label: Ecoregionalization
 - name: ecoregion_brt_analysis
   owner: ecology
   revisions:
+  - 2129484beb61
   - f0d6938d0451
   - f8962f1c832a
   - fc621f3f8226
@@ -1588,6 +1599,7 @@ tools:
 - name: ecoregion_taxa_seeker
   owner: ecology
   revisions:
+  - 18c4cd785a74
   - 788b118910a7
   - 9dc992f80c25
   - e3cd588fd14a
@@ -1598,10 +1610,12 @@ tools:
   - 374555fc30bd
   - 3d750279158b
   - b38b954b92b9
+  - c6b1bf7b0ac6
   tool_panel_section_label: Ecoregionalization
 - name: ecoregion_cluster_estimate
   owner: ecology
   revisions:
+  - 001d7d101915
   - 0f6542d0986e
   - 1b9522671e90
   - e94a25eed489
@@ -1611,6 +1625,7 @@ tools:
   revisions:
   - 24a81631a8b5
   - 32849c52aa54
+  - 844b5bf84164
   - edb8d19735a6
   tool_panel_section_label: Ecoregionalization
 - name: map_shp
diff --git a/eirene.yaml.lock b/eirene.yaml.lock
index fac152b4..586da17d 100644
--- a/eirene.yaml.lock
+++ b/eirene.yaml.lock
@@ -494,42 +494,50 @@ tools:
 - name: mfassignr_snplot
   owner: recetox
   revisions:
+  - 434fa3233e96
   - 7579b0cda787
   tool_panel_section_label: Metabolomics
 - name: mfassignr_histnoise
   owner: recetox
   revisions:
+  - 12b63108d645
   - 5d99cb9755da
   tool_panel_section_label: Metabolomics
 - name: mfassignr_kmdnoise
   owner: recetox
   revisions:
+  - 39a642fc9638
   - 99d021734000
   tool_panel_section_label: Metabolomics
 - name: mfassignr_isofiltr
   owner: recetox
   revisions:
   - e4ddc3bc7e15
+  - e7ef7718505d
   tool_panel_section_label: Metabolomics
 - name: mfassignr_mfassign
   owner: recetox
   revisions:
   - 9cbbfd54d7c4
+  - d5745e78fcfe
   tool_panel_section_label: Metabolomics
 - name: mfassignr_mfassigncho
   owner: recetox
   revisions:
+  - b96a462d9c3f
   - db058392cb2e
   tool_panel_section_label: Metabolomics
 - name: mfassignr_recal
   owner: recetox
   revisions:
   - 13ef8b748af9
+  - a3113a7c1767
   tool_panel_section_label: Metabolomics
 - name: mfassignr_recallist
   owner: recetox
   revisions:
   - 7e5ccc8b6f6e
+  - ddb9d330ecc0
   tool_panel_section_label: Metabolomics
 - name: rcx_tk
   owner: recetox
diff --git a/tools_galaxyp.yaml.lock b/tools_galaxyp.yaml.lock
index 14dfe471..c38fe8b0 100644
--- a/tools_galaxyp.yaml.lock
+++ b/tools_galaxyp.yaml.lock
@@ -5,6 +5,7 @@ tools:
 - name: fragpipe
   owner: galaxyp
   revisions:
+  - da9ebef968bd
   - ef46866326ef
   tool_panel_section_label: Proteomics
 - name: zeiss_lmd_converter
diff --git a/tools_iuc.yaml.lock b/tools_iuc.yaml.lock
index e2265318..440dafbe 100644
--- a/tools_iuc.yaml.lock
+++ b/tools_iuc.yaml.lock
@@ -18,6 +18,7 @@ tools:
   owner: iuc
   revisions:
   - 5aaffb8d8161
+  - e909d3bc4687
   tool_panel_section_label: Annotation
 - name: amrfinderplus
   owner: iuc
@@ -567,6 +568,7 @@ tools:
   revisions:
   - 2b970db61912
   - 3f6e5c701945
+  - 5f8efb080f49
   - dddd7ef63469
   tool_panel_section_label: Annotation
 - name: mirmachine
@@ -1649,6 +1651,7 @@ tools:
   owner: iuc
   revisions:
   - 0b663ca9a961
+  - 18dbde5680c0
   - 3d07b8a6dd8c
   - 7d3cd2087698
   - b9ea85dfaf45
@@ -2154,6 +2157,7 @@ tools:
 - name: falco
   owner: iuc
   revisions:
+  - babbcf02d35c
   - da336e3ead38
   - e462044ece67
   - eee1a2f6abd8
@@ -4039,11 +4043,13 @@ tools:
   revisions:
   - 9ed513717fc4
   - afc795d10918
+  - e30bc6da7a36
   - f801b844f239
   tool_panel_section_label: Metagenomic Analysis
 - name: cami_amber_add
   owner: iuc
   revisions:
+  - 04f8949026bf
   - 2e6ddf48a213
   - 433fb72344cb
   - b07cfe3b877e
@@ -4054,6 +4060,7 @@ tools:
   - 848594e0be6a
   - 8754ed6f0096
   - 8f0e53330d8e
+  - bc40aa3adf28
   tool_panel_section_label: Metagenomic Analysis
 - name: name2taxid
   owner: iuc
@@ -4069,6 +4076,7 @@ tools:
   owner: iuc
   revisions:
   - 1e10251b9615
+  - 8d0b2def5e65
   - d368e312aebd
   tool_panel_section_label: Metagenomic Analysis
 - name: krakentools_kreport2krona
@@ -4544,6 +4552,7 @@ tools:
   - 025b0113ee97
   - 150ebe4d0fd9
   - 254cb00a578f
+  - 25a5fa5f86a5
   - 4212f20315e5
   - 46fc97bb98f9
   - 487da152fb43
@@ -4795,6 +4804,7 @@ tools:
   - b4c750fe0fe3
   - b6ecdfac241f
   - c11805a111ea
+  - db58d5898fea
   tool_panel_section_label: Metagenomic Analysis
 - name: fasta_to_contig2bin
   owner: iuc
@@ -4818,6 +4828,7 @@ tools:
 - name: gtdbtk_classify_wf
   owner: iuc
   revisions:
+  - 65d52c693b8e
   - a68b985913ab
   tool_panel_section_label: Metagenomic Analysis
 - name: humann
@@ -5249,6 +5260,7 @@ tools:
   - 43ccbef89f1d
   - c629e6de3c49
   - ef2cace85809
+  - f4580402a2a2
   - faacef62bb54
   tool_panel_section_label: Metagenomic Analysis
 - name: malt_run
@@ -5343,6 +5355,7 @@ tools:
   - 27258eb73f0c
   - 2e5ae05160e0
   - 327d9f4cc95f
+  - 3cc4a60615c0
   - 3f05bf162005
   - 4fd3b5d8706b
   - 7f5d7b0e9884
@@ -5386,6 +5399,7 @@ tools:
   - b6897977d13e
   - b89b0765695d
   - ec368db926f4
+  - ef65b083bd0c
   - f5df500fcc3c
   - fd69c607b43f
   - ff8f55893e7d
@@ -5589,10 +5603,12 @@ tools:
   - 77c3ef9b0ed7
   - 88ebde55bef8
   - e889010415a1
+  - f8ebd1e802d7
   tool_panel_section_label: Metagenomic Analysis
 - name: virannot_otu
   owner: iuc
   revisions:
+  - 40fb54cc6628
   - 6838c2fd1228
   - 735a21808348
   - c9dac9b2e01c
@@ -5602,6 +5618,7 @@ tools:
   revisions:
   - 84d20d9c292d
   - bbaa89f070f4
+  - d1fd5579469d
   - fd7104249a3c
   tool_panel_section_label: Metagenomic Analysis
 - name: vsearch
@@ -7291,6 +7308,7 @@ tools:
 - name: clair3
   owner: iuc
   revisions:
+  - 3843a30053ee
   - 44f6ec903688
   - 63e02ef6e153
   - c8ba8286e7c0
@@ -9389,6 +9407,7 @@ tools:
 - name: samtools_ampliconclip
   owner: iuc
   revisions:
+  - 4967154b9859
   - 5f3ea90dc6ae
   - 6a8febad1f6c
   - a941babb9268
@@ -9407,6 +9426,7 @@ tools:
   revisions:
   - 06dc50b7b711
   - 1ebb4ecdc1ef
+  - 26b4f9f98aca
   - 33208952b99d
   - 3d873744df7e
   - 92ec40abcdcf
@@ -9437,6 +9457,7 @@ tools:
   - 720217c23995
   - a8d69aee190e
   - b3d99709fe1a
+  - b906586a6596
   tool_panel_section_label: SAM/BAM
 - name: samtools_fixmate
   owner: iuc
@@ -9444,6 +9465,7 @@ tools:
   - 41e36c99a008
   - 595ae1ba934a
   - bc0cc7bfbfe9
+  - d2df79922531
   - e5ece8fa99de
   tool_panel_section_label: SAM/BAM
 - name: samtools_flagstat
@@ -9471,6 +9493,7 @@ tools:
 - name: samtools_markdup
   owner: iuc
   revisions:
+  - 40fa6c240105
   - 83b8e36e9cbe
   - 887e02a45734
   - 8c440c3002bc
@@ -9488,6 +9511,7 @@ tools:
   - 740ce0a18f0d
   - 8890e2d4c068
   - b40e2d865d52
+  - cae2794d2deb
   tool_panel_section_label: SAM/BAM
 - name: samtools_mpileup
   owner: devteam
@@ -9514,6 +9538,7 @@ tools:
   revisions:
   - 020e144b5f78
   - 30388d878f81
+  - 85e38b31e8b3
   - bb8cfc6f6e0c
   - d7b4851d1971
   - db000c6007a0
@@ -9532,6 +9557,7 @@ tools:
   - 68ba55e96489
   - a4a10c7924d1
   - b5c88b7b153e
+  - b8beef827165
   tool_panel_section_label: SAM/BAM
 - name: samtools_sort
   owner: devteam
@@ -9540,6 +9566,7 @@ tools:
   - a430da4f04cd
   - a577ea614bed
   - cab3f8d35989
+  - d54a4df48867
   - e613c1ad4c4c
   - f56bdb93ae58
   tool_panel_section_label: SAM/BAM
@@ -9549,6 +9576,7 @@ tools:
   - 135c85f4cfaf
   - 57f3e32f809d
   - 5d9ae78f34d3
+  - 818030fa6bbf
   - b7f7826ef1cd
   - bcedabb53ddf
   - bd850490c7f1
@@ -9561,6 +9589,7 @@ tools:
   - 24c5d43cb545
   - 3a0efe14891f
   - 47035d167365
+  - 541082d03bef
   - 5a08c09b9311
   - 793ad847121d
   - 8cfc17e27132
@@ -9573,6 +9602,7 @@ tools:
   revisions:
   - 0dbf49c414ae
   - 2dce91e11ca7
+  - 32dc5f781059
   - 5826298f6a73
   - 6be888be75f9
   - b01db2684fa5
@@ -9689,6 +9719,7 @@ tools:
   - a9ab1b0a00dd
   - c0b037b12765
   - c5ac926c838f
+  - cfaf5a405371
   - e0395cca2c57
   - e1c3c2f2a834
   - fcb7370e827f
@@ -9707,6 +9738,7 @@ tools:
   - ae1e5d9d8972
   - b5c7ba11401d
   - cfc3f5a57dc6
+  - d330b3082107
   - e175d4067b00
   - fb9e030ffae4
   tool_panel_section_label: Single-cell
@@ -9715,6 +9747,7 @@ tools:
   revisions:
   - 038e32885fec
   - 05304c5c195d
+  - 0bf7fddf90c7
   - 286a24ac079c
   - 383dcb0500f9
   - 39e945f0b2c1
@@ -9735,6 +9768,7 @@ tools:
   - 4000634ece52
   - 43cb7b5a6fe7
   - 6db1b06e6bbb
+  - 7e8c677a7b71
   - 8db95f488f0f
   - 9bd945a03d7b
   - a56baceb1900
@@ -9760,6 +9794,7 @@ tools:
   owner: iuc
   revisions:
   - 05631436cdf1
+  - 0f1aaff9b22d
   - 4b0adaa31c95
   - 59be31ac9dc3
   - 7784821452ac
@@ -9837,6 +9872,7 @@ tools:
   owner: iuc
   revisions:
   - 0e212e42ef88
+  - 178242b82297
   - 20cfb9f3dded
   - 35bc2eb568ed
   - 3e4e1cf73d98
@@ -9864,6 +9900,7 @@ tools:
   - 5511647110ff
   - 6a76b60e05f5
   - 6ea5a05a260a
+  - 713a0c65b1fe
   - 72a6bebab2a5
   - 8b9610ab366a
   - a03ff8633507
@@ -9879,6 +9916,7 @@ tools:
   owner: iuc
   revisions:
   - 08192eebb47d
+  - 18262103fa61
   - 3081ff5c84a3
   - 5c3ebe2adc77
   - 5d2e17328afe
@@ -9903,6 +9941,7 @@ tools:
   - 51d945eab1e1
   - 5342ce58cd1e
   - 55f2212bb675
+  - 5dada6f76047
   - 7b9fafe32c86
   - 8e0f141c8c66
   - 94c19fb1281c
@@ -9921,6 +9960,7 @@ tools:
   owner: iuc
   revisions:
   - 1072ce66b426
+  - 2dfb2227a16c
   - 397d2c97af05
   - 4bfb75bb7c8e
   - 6adf98e782f3
@@ -9952,6 +9992,7 @@ tools:
   - 9ca360dde8e3
   - a39040ae0a38
   - a89ee42625ad
+  - b70219da4a96
   - bf2017df9837
   - c2ef03559dc6
   - c65fce500915
@@ -11961,6 +12002,7 @@ tools:
   owner: iuc
   revisions:
   - 0cb27ea69dc1
+  - 2c61c30a57e7
   - 4ba60cb14cb0
   - 5fe20c915fa6
   - 9c43baa60906
@@ -12001,6 +12043,7 @@ tools:
   revisions:
   - 10232d2b5062
   - 2814c058a087
+  - df84aaed4769
   - e7b39a7e0024
 - name: deeptools_alignmentsieve
   owner: bgruening