From f85f99e277378ee55df953ac3a930b8394d2075e Mon Sep 17 00:00:00 2001
From: Delphine Lariviere <lariviere.delphine@gmail.com>
Date: Tue, 3 Dec 2024 12:44:49 -0500
Subject: [PATCH] Add trimmed read collections as outputs and change busco gene
 predictor

---
 .../Scaffolding-HiC-VGP8.ga                   | 508 +++++++++---------
 1 file changed, 254 insertions(+), 254 deletions(-)

diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga
index 595caa648..801c7abb4 100644
--- a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga
+++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga
@@ -37,8 +37,8 @@
             "name": "Input dataset",
             "outputs": [],
             "position": {
-                "left": 0,
-                "top": 0
+                "left": 0.0,
+                "top": 76.92790836919438
             },
             "tool_id": null,
             "tool_state": "{\"optional\": false, \"tag\": \"\"}",
@@ -64,8 +64,8 @@
             "name": "Input parameter",
             "outputs": [],
             "position": {
-                "left": 22.331804896556207,
-                "top": 72.87824699895063
+                "left": 52.64642594523511,
+                "top": 179.09527251118433
             },
             "tool_id": null,
             "tool_state": "{\"restrictions\": [\"hap1\", \"hap2\", \"mat\", \"pat\", \"pri\", \"alt\"], \"parameter_type\": \"text\", \"optional\": false}",
@@ -84,21 +84,21 @@
             "inputs": [
                 {
                     "description": "",
-                    "name": "Sequence graph"
+                    "name": "Hi-C forward reads"
                 }
             ],
-            "label": "Sequence graph",
-            "name": "Input dataset",
+            "label": "Hi-C forward reads",
+            "name": "Input dataset collection",
             "outputs": [],
             "position": {
-                "left": 54.110429372176796,
-                "top": 150.61526811796614
+                "left": 80.99121632462999,
+                "top": 292.6877280640801
             },
             "tool_id": null,
-            "tool_state": "{\"optional\": true, \"tag\": \"\"}",
+            "tool_state": "{\"optional\": false, \"format\": [\"fastq.gz\"], \"tag\": null, \"collection_type\": \"list\"}",
             "tool_version": null,
-            "type": "data_input",
-            "uuid": "13cd4c1c-968b-4077-9845-e06738a2efb8",
+            "type": "data_collection_input",
+            "uuid": "e870fb7d-3b13-4dcf-85d5-33b3f78f66b3",
             "when": null,
             "workflow_outputs": []
         },
@@ -111,48 +111,48 @@
             "inputs": [
                 {
                     "description": "",
-                    "name": "Trim Hi-C Data?"
+                    "name": "Hi-C reverse reads"
                 }
             ],
-            "label": "Trim Hi-C Data?",
-            "name": "Input parameter",
+            "label": "Hi-C reverse reads",
+            "name": "Input dataset collection",
             "outputs": [],
             "position": {
-                "left": 105.43889348241458,
-                "top": 299.3556959439136
+                "left": 93.48378333854615,
+                "top": 395.9064331087657
             },
             "tool_id": null,
-            "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}",
+            "tool_state": "{\"optional\": false, \"format\": [\"fastq.gz\"], \"tag\": null, \"collection_type\": \"list\"}",
             "tool_version": null,
-            "type": "parameter_input",
-            "uuid": "68c2f24e-7f3f-40f9-b0dc-bbdd9ca46874",
+            "type": "data_collection_input",
+            "uuid": "bd83df79-71f9-40e3-815b-192da68f2067",
             "when": null,
             "workflow_outputs": []
         },
         "4": {
-            "annotation": "",
+            "annotation": "Trim 5 bases at the beginning of each read. Use with Arima Hi-C data if the Hi-C map looks \"noisy\".  (Select No if you are using the trimmed data generated by a previous workflow)",
             "content_id": null,
             "errors": null,
             "id": 4,
             "input_connections": {},
             "inputs": [
                 {
-                    "description": "",
-                    "name": "Collection Hi-C forward reads"
+                    "description": "Trim 5 bases at the beginning of each read. Use with Arima Hi-C data if the Hi-C map looks \"noisy\".  (Select No if you are using the trimmed data generated by a previous workflow)",
+                    "name": "Trim Hi-C Data?"
                 }
             ],
-            "label": "Collection Hi-C forward reads",
-            "name": "Input dataset collection",
+            "label": "Trim Hi-C Data?",
+            "name": "Input parameter",
             "outputs": [],
             "position": {
-                "left": 144.12739035406653,
-                "top": 488.44059813676193
+                "left": 149.03005061510206,
+                "top": 532.6527581425105
             },
             "tool_id": null,
-            "tool_state": "{\"optional\": false, \"format\": [\"fastq.gz\"], \"tag\": null, \"collection_type\": \"list\"}",
+            "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}",
             "tool_version": null,
-            "type": "data_collection_input",
-            "uuid": "e870fb7d-3b13-4dcf-85d5-33b3f78f66b3",
+            "type": "parameter_input",
+            "uuid": "68c2f24e-7f3f-40f9-b0dc-bbdd9ca46874",
             "when": null,
             "workflow_outputs": []
         },
@@ -162,33 +162,6 @@
             "errors": null,
             "id": 5,
             "input_connections": {},
-            "inputs": [
-                {
-                    "description": "",
-                    "name": "Collection Hi-C reverse reads"
-                }
-            ],
-            "label": "Collection Hi-C reverse reads",
-            "name": "Input dataset collection",
-            "outputs": [],
-            "position": {
-                "left": 173.3285643388762,
-                "top": 598.0446319159975
-            },
-            "tool_id": null,
-            "tool_state": "{\"optional\": false, \"format\": [\"fastq.gz\"], \"tag\": null, \"collection_type\": \"list\"}",
-            "tool_version": null,
-            "type": "data_collection_input",
-            "uuid": "bd83df79-71f9-40e3-815b-192da68f2067",
-            "when": null,
-            "workflow_outputs": []
-        },
-        "6": {
-            "annotation": "",
-            "content_id": null,
-            "errors": null,
-            "id": 6,
-            "input_connections": {},
             "inputs": [
                 {
                     "description": "",
@@ -199,8 +172,8 @@
             "name": "Input parameter",
             "outputs": [],
             "position": {
-                "left": 177.0207450496357,
-                "top": 695.9064787691357
+                "left": 198.68212514468095,
+                "top": 658.0505956837569
             },
             "tool_id": null,
             "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
@@ -210,11 +183,11 @@
             "when": null,
             "workflow_outputs": []
         },
-        "7": {
+        "6": {
             "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis\n",
             "content_id": null,
             "errors": null,
-            "id": 7,
+            "id": 6,
             "input_connections": {},
             "inputs": [
                 {
@@ -226,8 +199,8 @@
             "name": "Input parameter",
             "outputs": [],
             "position": {
-                "left": 226.5395435180352,
-                "top": 799.0259115230034
+                "left": 233.56649628363712,
+                "top": 759.2727153500458
             },
             "tool_id": null,
             "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
@@ -237,11 +210,11 @@
             "when": null,
             "workflow_outputs": []
         },
-        "8": {
+        "7": {
             "annotation": "Restriction enzymes used in preparation of Hi-C libraries.",
             "content_id": null,
             "errors": null,
-            "id": 8,
+            "id": 7,
             "input_connections": {},
             "inputs": [
                 {
@@ -253,8 +226,8 @@
             "name": "Input parameter",
             "outputs": [],
             "position": {
-                "left": 248.70923771663763,
-                "top": 867.1870851977436
+                "left": 275.0487484941569,
+                "top": 842.8875224115826
             },
             "tool_id": null,
             "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
@@ -264,11 +237,11 @@
             "when": null,
             "workflow_outputs": []
         },
-        "9": {
+        "8": {
             "annotation": "Estimated genome size from contiging workflow",
             "content_id": null,
             "errors": null,
-            "id": 9,
+            "id": 8,
             "input_connections": {},
             "inputs": [
                 {
@@ -280,8 +253,8 @@
             "name": "Input dataset",
             "outputs": [],
             "position": {
-                "left": 265.9677693731469,
-                "top": 996.0895047874516
+                "left": 311.41293024783795,
+                "top": 952.4744046620489
             },
             "tool_id": null,
             "tool_state": "{\"optional\": false, \"tag\": \"\"}",
@@ -291,11 +264,11 @@
             "when": null,
             "workflow_outputs": []
         },
-        "10": {
+        "9": {
             "annotation": "",
             "content_id": null,
             "errors": null,
-            "id": 10,
+            "id": 9,
             "input_connections": {},
             "inputs": [
                 {
@@ -307,8 +280,8 @@
             "name": "Input dataset",
             "outputs": [],
             "position": {
-                "left": 276.71776371799166,
-                "top": 1100.2434366748344
+                "left": 350.84345667959286,
+                "top": 1061.7661726031934
             },
             "tool_id": null,
             "tool_state": "{\"optional\": true, \"tag\": \"\"}",
@@ -318,6 +291,33 @@
             "when": null,
             "workflow_outputs": []
         },
+        "10": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 10,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "Sequence graph"
+                }
+            ],
+            "label": "Sequence graph",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 405.0717535399455,
+                "top": 1142.371927585886
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": true, \"tag\": \"\"}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "13cd4c1c-968b-4077-9845-e06738a2efb8",
+            "when": null,
+            "workflow_outputs": []
+        },
         "11": {
             "annotation": "",
             "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
@@ -339,8 +339,8 @@
                 }
             ],
             "position": {
-                "left": 728.9031059742254,
-                "top": 281.8870309575916
+                "left": 730.667899280956,
+                "top": 208.05868740916983
             },
             "post_job_actions": {},
             "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
@@ -364,7 +364,7 @@
             "id": 12,
             "input_connections": {
                 "input": {
-                    "id": 4,
+                    "id": 2,
                     "output_name": "output"
                 }
             },
@@ -378,8 +378,8 @@
                 }
             ],
             "position": {
-                "left": 496.92069224336444,
-                "top": 478.70095122138775
+                "left": 523.2602030208838,
+                "top": 454.40138843522675
             },
             "post_job_actions": {
                 "HideDatasetActionoutput": {
@@ -403,7 +403,7 @@
             "id": 13,
             "input_connections": {
                 "input": {
-                    "id": 5,
+                    "id": 3,
                     "output_name": "output"
                 }
             },
@@ -417,8 +417,8 @@
                 }
             ],
             "position": {
-                "left": 507.07754020980315,
-                "top": 632.6334176870486
+                "left": 533.4170509873225,
+                "top": 608.3338549008876
             },
             "post_job_actions": {
                 "HideDatasetActionoutput": {
@@ -442,7 +442,7 @@
             "id": 14,
             "input_connections": {
                 "input1": {
-                    "id": 9,
+                    "id": 8,
                     "output_name": "output"
                 }
             },
@@ -456,8 +456,8 @@
                 }
             ],
             "position": {
-                "left": 2758.4413884635774,
-                "top": 1775.1028116748344
+                "left": 2784.7808992410964,
+                "top": 1750.8032488886734
             },
             "post_job_actions": {
                 "HideDatasetActioninteger_param": {
@@ -485,7 +485,7 @@
                     "output_name": "output"
                 },
                 "mode_condition|swiss_army_knife": {
-                    "id": 10,
+                    "id": 9,
                     "output_name": "output"
                 }
             },
@@ -499,8 +499,8 @@
                 }
             ],
             "position": {
-                "left": 703.3689091223731,
-                "top": 24.29956278616098
+                "left": 729.7084198998924,
+                "top": 0.0
             },
             "post_job_actions": {},
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0",
@@ -518,99 +518,21 @@
             "workflow_outputs": []
         },
         "16": {
-            "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
-            "errors": null,
-            "id": 16,
-            "input_connections": {
-                "input_list": {
-                    "id": 12,
-                    "output_name": "output"
-                }
-            },
-            "inputs": [],
-            "label": "Hi-C Forward reads",
-            "name": "Collapse Collection",
-            "outputs": [
-                {
-                    "name": "output",
-                    "type": "input"
-                }
-            ],
-            "position": {
-                "left": 760.1600762569069,
-                "top": 520.9116755010011
-            },
-            "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
-            "tool_shed_repository": {
-                "changeset_revision": "90981f86000f",
-                "name": "collapse_collections",
-                "owner": "nml",
-                "tool_shed": "toolshed.g2.bx.psu.edu"
-            },
-            "tool_state": "{\"filename\": {\"add_name\": false, \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "5.1.0",
-            "type": "tool",
-            "uuid": "c645e225-f8e7-4cd8-addc-81f057eca9a4",
-            "when": null,
-            "workflow_outputs": []
-        },
-        "17": {
-            "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
-            "errors": null,
-            "id": 17,
-            "input_connections": {
-                "input_list": {
-                    "id": 13,
-                    "output_name": "output"
-                }
-            },
-            "inputs": [],
-            "label": "Hi-C Reverse reads",
-            "name": "Collapse Collection",
-            "outputs": [
-                {
-                    "name": "output",
-                    "type": "input"
-                }
-            ],
-            "position": {
-                "left": 747.1553922445268,
-                "top": 689.9519927249873
-            },
-            "post_job_actions": {},
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
-            "tool_shed_repository": {
-                "changeset_revision": "90981f86000f",
-                "name": "collapse_collections",
-                "owner": "nml",
-                "tool_shed": "toolshed.g2.bx.psu.edu"
-            },
-            "tool_state": "{\"filename\": {\"add_name\": false, \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "5.1.0",
-            "type": "tool",
-            "uuid": "57daf544-f77e-4fed-9024-30a49cbf9699",
-            "when": null,
-            "workflow_outputs": []
-        },
-        "18": {
             "annotation": "",
             "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1",
             "errors": null,
-            "id": 18,
+            "id": 16,
             "input_connections": {
                 "library|input_1": {
-                    "id": 16,
+                    "id": 12,
                     "output_name": "output"
                 },
                 "library|input_2": {
-                    "id": 17,
+                    "id": 13,
                     "output_name": "output"
                 },
                 "when": {
-                    "id": 3,
+                    "id": 4,
                     "output_name": "output"
                 }
             },
@@ -628,8 +550,8 @@
                 }
             ],
             "position": {
-                "left": 1027.394054488582,
-                "top": 498.9507440679115
+                "left": 778.3168770990734,
+                "top": 728.3399573421472
             },
             "post_job_actions": {
                 "RenameDatasetActionout1": {
@@ -657,7 +579,7 @@
             "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"1\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"paired\", \"__current_case__\": 1, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"input_2\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": []}, \"r2\": {\"adapters2\": [], \"front_adapters2\": [], \"anywhere_adapters2\": []}, \"pair_adapters\": false}, \"other_trimming_options\": {\"cut\": \"5\", \"cut2\": \"5\", \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": null, \"read_mod_options\": {\"strip_suffix\": null, \"length_tag\": null, \"rename\": null, \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "4.9+galaxy1",
             "type": "tool",
-            "uuid": "875236ba-4c3e-4a5d-b9a2-bd4aefa0ca3a",
+            "uuid": "74dab665-81f8-4d50-b389-83eb6f5ae9a3",
             "when": "$(inputs.when)",
             "workflow_outputs": [
                 {
@@ -672,18 +594,18 @@
                 }
             ]
         },
-        "19": {
+        "17": {
             "annotation": "",
             "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0",
             "errors": null,
-            "id": 19,
+            "id": 17,
             "input_connections": {
                 "style_cond|type_cond|pick_from_0|value": {
-                    "id": 18,
+                    "id": 16,
                     "output_name": "out1"
                 },
                 "style_cond|type_cond|pick_from_1|value": {
-                    "id": 16,
+                    "id": 12,
                     "output_name": "output"
                 }
             },
@@ -697,8 +619,8 @@
                 }
             ],
             "position": {
-                "left": 1294.1564739298656,
-                "top": 662.2742896647909
+                "left": 1048.6332433212092,
+                "top": 599.9820849007882
             },
             "post_job_actions": {},
             "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0",
@@ -715,18 +637,18 @@
             "when": null,
             "workflow_outputs": []
         },
-        "20": {
+        "18": {
             "annotation": "",
             "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0",
             "errors": null,
-            "id": 20,
+            "id": 18,
             "input_connections": {
                 "style_cond|type_cond|pick_from_0|value": {
-                    "id": 18,
+                    "id": 16,
                     "output_name": "out2"
                 },
                 "style_cond|type_cond|pick_from_1|value": {
-                    "id": 17,
+                    "id": 13,
                     "output_name": "output"
                 }
             },
@@ -740,8 +662,8 @@
                 }
             ],
             "position": {
-                "left": 1265.0869012069427,
-                "top": 860.695120414965
+                "left": 1066.4952671523822,
+                "top": 839.8214165857199
             },
             "post_job_actions": {},
             "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0",
@@ -758,6 +680,84 @@
             "when": null,
             "workflow_outputs": []
         },
+        "19": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+            "errors": null,
+            "id": 19,
+            "input_connections": {
+                "input_list": {
+                    "id": 17,
+                    "output_name": "data_param"
+                }
+            },
+            "inputs": [],
+            "label": "Hi-C Forward reads",
+            "name": "Collapse Collection",
+            "outputs": [
+                {
+                    "name": "output",
+                    "type": "input"
+                }
+            ],
+            "position": {
+                "left": 1359.4891551666378,
+                "top": 414.8924775558669
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+            "tool_shed_repository": {
+                "changeset_revision": "90981f86000f",
+                "name": "collapse_collections",
+                "owner": "nml",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"filename\": {\"add_name\": false, \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.1.0",
+            "type": "tool",
+            "uuid": "c645e225-f8e7-4cd8-addc-81f057eca9a4",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "20": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+            "errors": null,
+            "id": 20,
+            "input_connections": {
+                "input_list": {
+                    "id": 18,
+                    "output_name": "data_param"
+                }
+            },
+            "inputs": [],
+            "label": "Hi-C Reverse reads",
+            "name": "Collapse Collection",
+            "outputs": [
+                {
+                    "name": "output",
+                    "type": "input"
+                }
+            ],
+            "position": {
+                "left": 1350.6087780378298,
+                "top": 972.1845382221943
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0",
+            "tool_shed_repository": {
+                "changeset_revision": "90981f86000f",
+                "name": "collapse_collections",
+                "owner": "nml",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"filename\": {\"add_name\": false, \"__current_case__\": 1}, \"input_list\": {\"__class__\": \"ConnectedValue\"}, \"one_header\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "5.1.0",
+            "type": "tool",
+            "uuid": "57daf544-f77e-4fed-9024-30a49cbf9699",
+            "when": null,
+            "workflow_outputs": []
+        },
         "21": {
             "annotation": "",
             "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1",
@@ -766,7 +766,7 @@
             "input_connections": {
                 "fastq_input|fastq_input1": {
                     "id": 19,
-                    "output_name": "data_param"
+                    "output_name": "output"
                 },
                 "reference_source|ref_file": {
                     "id": 15,
@@ -783,8 +783,8 @@
                 }
             ],
             "position": {
-                "left": 1619.9079438762212,
-                "top": 575.9391636416469
+                "left": 1646.2474546537405,
+                "top": 551.6396008554859
             },
             "post_job_actions": {
                 "HideDatasetActionbam_output": {
@@ -815,7 +815,7 @@
             "input_connections": {
                 "fastq_input|fastq_input1": {
                     "id": 20,
-                    "output_name": "data_param"
+                    "output_name": "output"
                 },
                 "reference_source|ref_file": {
                     "id": 15,
@@ -832,8 +832,8 @@
                 }
             ],
             "position": {
-                "left": 1521.0379983117402,
-                "top": 1036.9934575029588
+                "left": 1646.4957607775193,
+                "top": 944.634030963839
             },
             "post_job_actions": {
                 "HideDatasetActionbam_output": {
@@ -881,8 +881,8 @@
                 }
             ],
             "position": {
-                "left": 1853.9101384635776,
-                "top": 834.2121866748344
+                "left": 1898.6673772412703,
+                "top": 800.2453744142445
             },
             "post_job_actions": {
                 "TagDatasetActionoutfile": {
@@ -928,8 +928,8 @@
                 }
             ],
             "position": {
-                "left": 2112.169383210396,
-                "top": 1062.220075997486
+                "left": 2138.508893987915,
+                "top": 1037.920513211325
             },
             "post_job_actions": {
                 "TagDatasetActionpretext_map_out": {
@@ -942,7 +942,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "79b48f02db49",
+                "changeset_revision": "c6cec5ab35c1",
                 "name": "pretext_map",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -961,7 +961,7 @@
             "id": 25,
             "input_connections": {
                 "function|agp": {
-                    "id": 2,
+                    "id": 10,
                     "output_name": "output"
                 },
                 "function|bfile": {
@@ -969,7 +969,7 @@
                     "output_name": "outfile"
                 },
                 "function|enzyme_conditional|preconfigured_enzymes": {
-                    "id": 8,
+                    "id": 7,
                     "output_name": "output"
                 },
                 "function|fasta": {
@@ -1007,8 +1007,8 @@
                 }
             ],
             "position": {
-                "left": 2582.0891841410785,
-                "top": 99.67444343495919
+                "left": 2608.4286949185976,
+                "top": 75.37488064879821
             },
             "post_job_actions": {
                 "TagDatasetActionfinal_agp_out": {
@@ -1074,8 +1074,8 @@
                 }
             ],
             "position": {
-                "left": 2382.2851384635774,
-                "top": 1052.3059366748344
+                "left": 2408.6246492410964,
+                "top": 1028.0063738886734
             },
             "post_job_actions": {
                 "HideDatasetActionpretext_snap_out": {
@@ -1130,8 +1130,8 @@
                 }
             ],
             "position": {
-                "left": 2885.00703880371,
-                "top": 303.86249764382023
+                "left": 2911.3465495812293,
+                "top": 279.56293485765923
             },
             "post_job_actions": {},
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
@@ -1169,8 +1169,8 @@
                 }
             ],
             "position": {
-                "left": 2752.5038884635774,
-                "top": 1171.7434366748344
+                "left": 2778.8433992410964,
+                "top": 1147.4438738886734
             },
             "post_job_actions": {
                 "TagDatasetActionoutput": {
@@ -1220,8 +1220,8 @@
                 }
             ],
             "position": {
-                "left": 3134.436829641301,
-                "top": 195.14777472213842
+                "left": 3160.77634041882,
+                "top": 170.84821193597745
             },
             "post_job_actions": {
                 "RenameDatasetActionoutput": {
@@ -1270,7 +1270,7 @@
                     "output_name": "output"
                 },
                 "mode_condition|swiss_army_knife": {
-                    "id": 10,
+                    "id": 9,
                     "output_name": "output"
                 }
             },
@@ -1284,8 +1284,8 @@
                 }
             ],
             "position": {
-                "left": 3405.7695134635774,
-                "top": 405.35281167483436
+                "left": 3432.1090242410964,
+                "top": 381.05324888867335
             },
             "post_job_actions": {
                 "TagDatasetActionoutput": {
@@ -1341,8 +1341,8 @@
                 }
             ],
             "position": {
-                "left": 3865.3007634635774,
-                "top": 1842.1340616748344
+                "left": 3891.6402742410964,
+                "top": 1817.8344988886734
             },
             "post_job_actions": {
                 "TagDatasetActionstats": {
@@ -1394,8 +1394,8 @@
                 }
             ],
             "position": {
-                "left": 3992.9570134635774,
-                "top": 1649.1028116748344
+                "left": 4019.2965242410964,
+                "top": 1624.8032488886734
             },
             "post_job_actions": {
                 "TagDatasetActionstats": {
@@ -1434,7 +1434,7 @@
             "input_connections": {
                 "fastq_input|fastq_input1": {
                     "id": 19,
-                    "output_name": "data_param"
+                    "output_name": "output"
                 },
                 "reference_source|ref_file": {
                     "id": 30,
@@ -1451,8 +1451,8 @@
                 }
             ],
             "position": {
-                "left": 3652.6601384635774,
-                "top": 631.3840616748344
+                "left": 3678.9996492410964,
+                "top": 607.0844988886734
             },
             "post_job_actions": {
                 "HideDatasetActionbam_output": {
@@ -1483,7 +1483,7 @@
             "input_connections": {
                 "fastq_input|fastq_input1": {
                     "id": 20,
-                    "output_name": "data_param"
+                    "output_name": "output"
                 },
                 "reference_source|ref_file": {
                     "id": 30,
@@ -1500,8 +1500,8 @@
                 }
             ],
             "position": {
-                "left": 3651.5038884635774,
-                "top": 909.1028116748344
+                "left": 3677.8433992410964,
+                "top": 884.8032488886734
             },
             "post_job_actions": {
                 "HideDatasetActionbam_output": {
@@ -1535,11 +1535,11 @@
                     "output_name": "output"
                 },
                 "lineage_conditional|cached_db": {
-                    "id": 6,
+                    "id": 5,
                     "output_name": "output"
                 },
                 "lineage|lineage_dataset": {
-                    "id": 7,
+                    "id": 6,
                     "output_name": "output"
                 }
             },
@@ -1565,8 +1565,8 @@
                 }
             ],
             "position": {
-                "left": 3938.583381985884,
-                "top": 325.9896080787381
+                "left": 3964.922892763403,
+                "top": 301.6900452925771
             },
             "post_job_actions": {
                 "TagDatasetActionbusco_missing": {
@@ -1605,7 +1605,7 @@
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"metaeuk\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": {\"__class__\": \"ConnectedValue\"}}, \"outputs\": [\"short_summary\", \"missing\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "5.7.1+galaxy0",
             "type": "tool",
             "uuid": "c30b907f-05c9-4709-a939-b66f52daf6e4",
@@ -1644,8 +1644,8 @@
                 }
             ],
             "position": {
-                "left": 4192.54582453431,
-                "top": 2034.4604286379645
+                "left": 4218.885335311829,
+                "top": 2010.1608658518035
             },
             "post_job_actions": {
                 "HideDatasetActionoutfile": {
@@ -1689,8 +1689,8 @@
             "name": "gfastats_data_prep",
             "outputs": [],
             "position": {
-                "left": 4525.816388463577,
-                "top": 1758.5403116748344
+                "left": 4552.155899241096,
+                "top": 1734.2407488886734
             },
             "subworkflow": {
                 "a_galaxy_workflow": "true",
@@ -2070,8 +2070,8 @@
                 }
             ],
             "position": {
-                "left": 3955.4882634635774,
-                "top": 908.3215616748344
+                "left": 3981.8277742410964,
+                "top": 884.0219988886734
             },
             "post_job_actions": {
                 "TagDatasetActionoutfile": {
@@ -2117,8 +2117,8 @@
                 }
             ],
             "position": {
-                "left": 5089.222638463577,
-                "top": 1485.3528116748344
+                "left": 5115.562149241096,
+                "top": 1461.0532488886734
             },
             "post_job_actions": {},
             "tool_id": "Cut1",
@@ -2150,8 +2150,8 @@
                 }
             ],
             "position": {
-                "left": 5091.253888463577,
-                "top": 1626.3371866748344
+                "left": 5117.593399241096,
+                "top": 1602.0376238886734
             },
             "post_job_actions": {
                 "HideDatasetActionout_file1": {
@@ -2189,8 +2189,8 @@
                 }
             ],
             "position": {
-                "left": 4294.347638463577,
-                "top": 1042.3059366748344
+                "left": 4320.687149241096,
+                "top": 1018.0063738886734
             },
             "post_job_actions": {
                 "TagDatasetActionpretext_map_out": {
@@ -2203,7 +2203,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "79b48f02db49",
+                "changeset_revision": "c6cec5ab35c1",
                 "name": "pretext_map",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -2236,8 +2236,8 @@
                 }
             ],
             "position": {
-                "left": 4436.535138463577,
-                "top": 801.9621866748344
+                "left": 4462.874649241096,
+                "top": 777.6626238886734
             },
             "post_job_actions": {
                 "HideDatasetActionoutput": {
@@ -2281,8 +2281,8 @@
                 }
             ],
             "position": {
-                "left": 5368.597638463577,
-                "top": 1408.0090616748344
+                "left": 5394.937149241096,
+                "top": 1383.7094988886734
             },
             "post_job_actions": {
                 "RenameDatasetActionoutput1": {
@@ -2341,8 +2341,8 @@
                 }
             ],
             "position": {
-                "left": 5360.316388463577,
-                "top": 1642.2278116748344
+                "left": 5386.655899241096,
+                "top": 1617.9282488886734
             },
             "post_job_actions": {
                 "RenameDatasetActionoutput1": {
@@ -2401,8 +2401,8 @@
                 }
             ],
             "position": {
-                "left": 4662.7149398000865,
-                "top": 1145.830358796189
+                "left": 4689.054450577606,
+                "top": 1121.530796010028
             },
             "post_job_actions": {
                 "HideDatasetActionpretext_snap_out": {
@@ -2453,8 +2453,8 @@
                 }
             ],
             "position": {
-                "left": 4749.839771488325,
-                "top": 471.03187535372973
+                "left": 4776.179282265844,
+                "top": 446.7323125675687
             },
             "post_job_actions": {
                 "TagDatasetActionoutfile": {
@@ -2500,8 +2500,8 @@
                 }
             ],
             "position": {
-                "left": 4927.035138463577,
-                "top": 1206.8996866748344
+                "left": 4953.374649241096,
+                "top": 1182.6001238886734
             },
             "post_job_actions": {
                 "TagDatasetActionoutput": {
@@ -2530,6 +2530,6 @@
     "tags": [
         "VGP_curated"
     ],
-    "uuid": "ac267fc0-1e7a-4d5a-9df5-fa5bae78a256",
-    "version": 3
+    "uuid": "d78ae0a0-9b49-4aa8-845a-4d7a3d49f7da",
+    "version": 7
 }