diff --git a/workflows/genome_annotation/lncRNAs-annotation/CHANGELOG.md b/workflows/genome_annotation/lncRNAs-annotation/CHANGELOG.md index f411fbc0c1..cf212e5e2d 100644 --- a/workflows/genome_annotation/lncRNAs-annotation/CHANGELOG.md +++ b/workflows/genome_annotation/lncRNAs-annotation/CHANGELOG.md @@ -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. \ No newline at end of file diff --git a/workflows/genome_annotation/lncRNAs-annotation/Galaxy-Workflow-lncRNAs_annotation_workflow.ga b/workflows/genome_annotation/lncRNAs-annotation/Galaxy-Workflow-lncRNAs_annotation_workflow.ga index ebd13809e8..ab919eed99 100644 --- a/workflows/genome_annotation/lncRNAs-annotation/Galaxy-Workflow-lncRNAs_annotation_workflow.ga +++ b/workflows/genome_annotation/lncRNAs-annotation/Galaxy-Workflow-lncRNAs_annotation_workflow.ga @@ -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" @@ -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", @@ -290,10 +290,6 @@ { "description": "runtime parameter for tool gffread", "name": "chr_replace" - }, - { - "description": "runtime parameter for tool gffread", - "name": "input" } ], "label": "gffread", @@ -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", @@ -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": { @@ -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, @@ -421,11 +419,11 @@ "name": "FEELnc", "outputs": [ { - "name": "lcnRNA annotation", + "name": "candidate_lncRNA", "type": "gtf" }, { - "name": "lcnRNA annotation", + "name": "candidate_mRNA", "type": "gtf" }, { @@ -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", @@ -485,7 +484,7 @@ }, "inputs": [], "label": "Concatenation step", - "name": "Concatenate datasets", + "name": "Concatenate multiple datasets or collections", "outputs": [ { "name": "out_file1", @@ -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", @@ -513,6 +513,7 @@ } }, "tags": [], - "uuid": "f6d6b63f-6fcc-42bb-bafb-12d9dd98983e", - "version": 1 + "uuid": "eb532d61-4b26-41e3-aaa8-d1f850907948", + "version": 1, + "release": "0.2" } \ No newline at end of file