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Merge pull request #654 from planemo-autoupdate/workflows/genome_anno…
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…tation/annotation-helixer

Updating workflows/genome_annotation/annotation-helixer from 0.1 to 0.2
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@bgruening
bgruening authored Jan 28, 2025
2 parents b08cc14 + a284298 commit 771a42e
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5 changes: 5 additions & 0 deletions workflows/genome_annotation/annotation-helixer/CHANGELOG.md
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# Changelog

## [0.2] 2025-01-27

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0`

## [0.1]

Initial version of the Helixer workflow for genome annotation
44 changes: 15 additions & 29 deletions workflows/genome_annotation/annotation-helixer/Galaxy-Workflow-annotation_helixer.ga
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],
"format-version": "0.1",
"license": "MIT",
"release": "0.1",
"release": "0.2",
"name": "Genome annotation with Helixer",
"report": {
"markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
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"inputs": [
{
"description": "Input dataset containing genomic sequences in FASTA format",
"name": "Input"
"name": "Genome sequence"
}
],
"label": "Genome sequence",
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},
"2": {
"annotation": "Completeness assessment of the genome using the Busco tool",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0",
"errors": null,
"id": 2,
"input_connections": {
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"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Busco",
"name": "input"
}
],
"inputs": [],
"label": "Busco on genome",
"name": "Busco",
"outputs": [
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"top": 942.4706486763349
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0",
"tool_shed_repository": {
"changeset_revision": "2babe6d5c561",
"changeset_revision": "e5c372c91e46",
"name": "busco",
"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\": \"augustus\", \"__current_case__\": 2, \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": false}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": \"mucorales_odb10\"}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": \"all+2024-03-21-114020\"}, \"outputs\": [\"short_summary\", \"image\", \"gff\", \"missing\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "5.7.1+galaxy0",
"tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"use_augustus\": {\"use_augustus_selector\": \"augustus\", \"__current_case__\": 2, \"aug_prediction\": {\"augustus_mode\": \"no\", \"__current_case__\": 0}, \"long\": false}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": \"mucorales_odb10\"}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": \"all+2024-03-21-114020\"}, \"outputs\": [\"short_summary\", \"image\", \"gff\", \"missing\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "5.8.0+galaxy0",
"type": "tool",
"uuid": "c0e4cca7-0bc3-4ef2-81b2-c990b1b77d87",
"when": null,
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},
"6": {
"annotation": "Completeness assessment of the genome using the Busco tool",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0",
"errors": null,
"id": 6,
"input_connections": {
Expand All @@ -465,12 +460,7 @@
"output_name": "output_pep"
}
},
"inputs": [
{
"description": "runtime parameter for tool Busco",
"name": "input"
}
],
"inputs": [],
"label": "Busco on protein",
"name": "Busco",
"outputs": [
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"top": 58.61198039869754
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0",
"tool_shed_repository": {
"changeset_revision": "2babe6d5c561",
"changeset_revision": "e5c372c91e46",
"name": "busco",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"prot\", \"__current_case__\": 2}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": \"mucorales_odb10\"}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": \"all+2024-03-21-114020\"}, \"outputs\": [\"short_summary\", \"image\", \"gff\", \"missing\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "5.7.1+galaxy0",
"tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"prot\", \"__current_case__\": 2}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": \"mucorales_odb10\"}, \"lineage_conditional\": {\"selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": \"all+2024-03-21-114020\"}, \"outputs\": [\"short_summary\", \"image\", \"gff\", \"missing\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "5.8.0+galaxy0",
"type": "tool",
"uuid": "51dcc6a4-ff87-4a98-98fa-de00ce54325f",
"when": null,
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}
},
"inputs": [
{
"description": "runtime parameter for tool OMArk",
"name": "input"
},
{
"description": "runtime parameter for tool OMArk",
"name": "input_iso"
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"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"database\": \"LUCA-v2.0.0.h5\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"input_iso\": {\"__class__\": \"RuntimeValue\"}, \"omark_mode\": false, \"outputs\": \"detail_sum\", \"r\": null, \"t\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"database\": \"LUCA-v2.0.0.h5\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"input_iso\": {\"__class__\": \"RuntimeValue\"}, \"omark_mode\": false, \"outputs\": \"detail_sum\", \"r\": null, \"t\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "0.3.0+galaxy2",
"type": "tool",
"uuid": "75e1dde7-5d60-4092-af57-cd7b065145e2",
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