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Updating workflows/genome_annotation/lncRNAs-annotation from 0.1 to 0.2 #1253

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Updating workflows/genome_annotation/lncRNAs-annotation from 0.1 to 0.2 #1253

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5 changes: 5 additions & 0 deletions workflows/genome_annotation/lncRNAs-annotation/CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
# Changelog

## [0.2] - 2026-06-08

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/3.0.3+galaxy1`

## [0.1] - 2025-03-05

Initial version of the lncRNAs annotation workflow.
33 changes: 17 additions & 16 deletions ...flows/genome_annotation/lncRNAs-annotation/Galaxy-Workflow-lncRNAs_annotation_workflow.ga
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Expand Up @@ -111,7 +111,6 @@
],
"format-version": "0.1",
"license": "MIT",
"release": "0.1",
"name": "lncRNAs annotation workflow",
"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"
Expand Down Expand Up @@ -269,6 +268,7 @@
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"--fr\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"--rf\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_uuid": null,
"tool_version": "0.2.0",
"type": "tool",
"uuid": "41e690b0-597b-4a3a-9289-5fc22fc6644b",
Expand All @@ -290,10 +290,6 @@
{
"description": "runtime parameter for tool gffread",
"name": "chr_replace"
},
{
"description": "runtime parameter for tool gffread",
"name": "input"
}
],
"label": "gffread",
Expand All @@ -316,7 +312,8 @@
"owner": "devteam",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"chr_replace\": {\"__class__\": \"RuntimeValue\"}, \"decode_url\": false, \"expose\": false, \"filtering\": null, \"full_gff_attribute_preservation\": false, \"gffs\": {\"gff_fmt\": \"gtf\", \"__current_case__\": 2, \"tname\": \"\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"maxintron\": null, \"merging\": {\"merge_sel\": \"none\", \"__current_case__\": 0}, \"reference_genome\": {\"source\": \"none\", \"__current_case__\": 0}, \"region\": {\"region_filter\": \"none\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"chr_replace\": {\"__class__\": \"RuntimeValue\"}, \"decode_url\": false, \"expose\": false, \"filtering\": null, \"full_gff_attribute_preservation\": false, \"gffs\": {\"gff_fmt\": \"gtf\", \"__current_case__\": 2, \"tname\": \"\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"maxintron\": null, \"merging\": {\"merge_sel\": \"none\", \"__current_case__\": 0}, \"reference_genome\": {\"source\": \"none\", \"__current_case__\": 0}, \"region\": {\"region_filter\": \"none\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
"tool_uuid": null,
"tool_version": "2.2.1.4+galaxy0",
"type": "tool",
"uuid": "1a2ed039-986a-47c0-bc76-7bb1509fad87",
Expand All @@ -331,7 +328,7 @@
},
"6": {
"annotation": "StringTie is a fast, highly efficient assembler of RNA-Seq alignments into potential transcripts. ",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/3.0.3+galaxy1",
"errors": null,
"id": 6,
"input_connections": {
Expand Down Expand Up @@ -377,15 +374,16 @@
"output_name": "output gtf"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/3.0.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "cbf488da3b2c",
"changeset_revision": "92198ab2345f",
"name": "stringtie",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adv\": {\"abundance_estimation\": false, \"omit_sequences\": \"\", \"name_prefix\": null, \"fraction\": \"0.01\", \"min_tlen\": \"200\", \"min_anchor_len\": \"10\", \"min_anchor_cov\": \"1\", \"min_bundle_cov\": \"1\", \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"multi_mapping\": false, \"point_features\": {\"__class__\": \"RuntimeValue\"}}, \"guide\": {\"use_guide\": \"yes\", \"__current_case__\": 1, \"guide_source\": {\"guide_gff_select\": \"history\", \"__current_case__\": 1, \"ref_hist\": {\"__class__\": \"ConnectedValue\"}}, \"input_estimation\": false, \"special_outputs\": {\"special_outputs_select\": \"no\", \"__current_case__\": 2}, \"coverage_file\": false}, \"input_options\": {\"input_mode\": \"short_reads\", \"__current_case__\": 0, \"input_bam\": {\"__class__\": \"ConnectedValue\"}}, \"rna_strandness\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.2.3+galaxy0",
"tool_state": "{\"adv\": {\"abundance_estimation\": false, \"omit_sequences\": \"\", \"name_prefix\": null, \"fraction\": \"0.01\", \"min_tlen\": \"200\", \"min_anchor_len\": \"10\", \"min_anchor_cov\": \"1\", \"min_bundle_cov\": \"1\", \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"multi_mapping\": false, \"point_features\": {\"__class__\": \"RuntimeValue\"}}, \"guide\": {\"use_guide\": \"yes\", \"__current_case__\": 1, \"guide_source\": {\"guide_gff_select\": \"history\", \"__current_case__\": 1, \"ref_hist\": {\"__class__\": \"ConnectedValue\"}}, \"input_estimation\": false, \"special_outputs\": {\"special_outputs_select\": \"no\", \"__current_case__\": 2}, \"coverage_file\": false}, \"input_options\": {\"input_mode\": \"short_reads\", \"__current_case__\": 0, \"input_bam\": {\"__class__\": \"ConnectedValue\"}}, \"nascent_mode\": \"\", \"rna_strandness\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_uuid": null,
"tool_version": "3.0.3+galaxy1",
"type": "tool",
"uuid": "632f7928-d838-4bbf-b0f9-6a94ea9eb427",
"when": null,
Expand Down Expand Up @@ -421,11 +419,11 @@
"name": "FEELnc",
"outputs": [
{
"name": "lcnRNA annotation",
"name": "candidate_lncRNA",
"type": "gtf"
},
{
"name": "lcnRNA annotation",
"name": "candidate_mRNA",
"type": "gtf"
},
{
Expand All @@ -446,6 +444,7 @@
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__input_ext\": \"input\", \"candidate\": {\"__class__\": \"ConnectedValue\"}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"genome\": {\"__class__\": \"ConnectedValue\"}, \"reference\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_uuid": null,
"tool_version": "0.2.1+galaxy0",
"type": "tool",
"uuid": "e7d02c0b-09a9-46e0-836a-048a3a5fdc33",
Expand Down Expand Up @@ -485,7 +484,7 @@
},
"inputs": [],
"label": "Concatenation step",
"name": "Concatenate datasets",
"name": "Concatenate multiple datasets or collections",
"outputs": [
{
"name": "out_file1",
Expand All @@ -499,6 +498,7 @@
"post_job_actions": {},
"tool_id": "cat1",
"tool_state": "{\"__input_ext\": \"gtf\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [{\"__index__\": 0, \"input2\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_uuid": null,
"tool_version": "1.0.0",
"type": "tool",
"uuid": "27355e91-6006-443f-af12-33b801ec371b",
Expand All @@ -513,6 +513,7 @@
}
},
"tags": [],
"uuid": "f6d6b63f-6fcc-42bb-bafb-12d9dd98983e",
"version": 1
"uuid": "eb532d61-4b26-41e3-aaa8-d1f850907948",
"version": 1,
"release": "0.2"
}
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