Skip to content

Commit

Permalink
Updating workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8 from 0.2.7 to…
Browse files Browse the repository at this point in the history 
… 0.2.8
  • Loading branch information
planemo-autoupdate committed Aug 22, 2024
1 parent 425856c commit 4f38eac
Show file tree
Hide file tree
Showing 2 changed files with 97 additions and 19 deletions.
5 changes: 5 additions & 0 deletions workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/CHANGELOG.md
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
# Changelog

## [0.2.8] 2024-08-22

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1`

## [0.2.7] 2024-08-13

- Expose Busco lineage database parameter
Expand Down
111 changes: 92 additions & 19 deletions workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8.ga
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
],
"format-version": "0.1",
"license": "CC-BY-4.0",
"release": "0.2.7",
"release": "0.2.8",
"name": "Scaffolding-HiC-VGP8",
"report": {
"markdown": "# Workflow Execution Report\n\nTime workflow was invoked\n\n```galaxy\ninvocation_time()\n```\n\n```galaxy\ngenerate_galaxy_version()\n```\n\n\n## BUSCO results (Vertebrata database)\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Busco Summary image\")\n```\n\n\n## Assembly statistics\n\n\n```galaxy\nhistory_dataset_as_table(output=\"clean_stats\")\n```\n\n\n## Nx and Size plots\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Nx Plot\")\n```\n\n\n```galaxy\nhistory_dataset_as_image(output=\"Size Plot\")\n```\n\n## PretextMap\n\n### Before Scaffolding\n\n\r\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Map Before HiC scaffolding\")\n```\r\n\n\n### After Scaffolding\r\n```galaxy\nhistory_dataset_as_image(output=\"Pretext Map After HiC scaffolding\")\n```\r\n\n\n\n\n## Current Workflow\n```galaxy\nworkflow_display()\n```\n"
Expand Down Expand Up @@ -318,7 +318,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool gfastats",
"name": "mode_condition"
}
],
"label": null,
"name": "gfastats",
"outputs": [
Expand Down Expand Up @@ -361,7 +366,16 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool BWA-MEM2",
"name": "fastq_input"
},
{
"description": "runtime parameter for tool BWA-MEM2",
"name": "reference_source"
}
],
"label": null,
"name": "BWA-MEM2",
"outputs": [
Expand Down Expand Up @@ -410,7 +424,16 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool BWA-MEM2",
"name": "fastq_input"
},
{
"description": "runtime parameter for tool BWA-MEM2",
"name": "reference_source"
}
],
"label": null,
"name": "BWA-MEM2",
"outputs": [
Expand Down Expand Up @@ -565,7 +588,20 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool YAHS",
"name": "function"
},
{
"description": "runtime parameter for tool YAHS",
"name": "function"
},
{
"description": "runtime parameter for tool YAHS",
"name": "function"
}
],
"label": null,
"name": "YAHS",
"outputs": [
Expand Down Expand Up @@ -708,7 +744,12 @@
"output_name": "final_agp_out"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool gfastats",
"name": "mode_condition"
}
],
"label": null,
"name": "gfastats",
"outputs": [
Expand Down Expand Up @@ -819,7 +860,12 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool gfastats",
"name": "mode_condition"
}
],
"label": null,
"name": "gfastats",
"outputs": [
Expand Down Expand Up @@ -986,7 +1032,16 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool BWA-MEM2",
"name": "fastq_input"
},
{
"description": "runtime parameter for tool BWA-MEM2",
"name": "reference_source"
}
],
"label": null,
"name": "BWA-MEM2",
"outputs": [
Expand Down Expand Up @@ -1035,7 +1090,16 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool BWA-MEM2",
"name": "fastq_input"
},
{
"description": "runtime parameter for tool BWA-MEM2",
"name": "reference_source"
}
],
"label": null,
"name": "BWA-MEM2",
"outputs": [
Expand Down Expand Up @@ -1088,7 +1152,16 @@
"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Busco",
"name": "lineage"
},
{
"description": "runtime parameter for tool Busco",
"name": "lineage_conditional"
}
],
"label": null,
"name": "Busco",
"outputs": [
Expand Down Expand Up @@ -1150,7 +1223,7 @@
"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, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__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, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__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": "5.5.0+galaxy0",
"type": "tool",
"uuid": "c30b907f-05c9-4709-a939-b66f52daf6e4",
Expand Down Expand Up @@ -1201,7 +1274,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -1343,7 +1416,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -1525,7 +1598,7 @@
},
"7": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1",
"errors": null,
"id": 7,
"input_connections": {
Expand Down Expand Up @@ -1560,15 +1633,15 @@
"output_name": "out_file1"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1",
"tool_shed_repository": {
"changeset_revision": "6595517c2dd8",
"changeset_revision": "aff5135563c6",
"name": "column_maker",
"owner": "devteam",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": {\"__class__\": \"ConnectedValue\"}, \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 1, \"cond\": \"c2/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 2, \"cond\": \"c3/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.0",
"tool_version": "2.1",
"type": "tool",
"uuid": "ee776542-b181-4dc3-8a15-eae6c1958292",
"when": null,
Expand All @@ -1582,7 +1655,7 @@
}
},
"tags": [],
"uuid": "b30c8dd0-24e7-4e74-ad9b-5fefd27893fa"
"uuid": "f8afc779-b45c-43f1-953e-68e5f6598ca5"
},
"tool_id": null,
"type": "subworkflow",
Expand Down Expand Up @@ -2012,7 +2085,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down

0 comments on commit 4f38eac

Please sign in to comment.