From 5c3ceef4abbd2280c9605aa007f1be82b055bb8f Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Tue, 24 Sep 2024 14:18:53 +0000 Subject: [PATCH] Updating workflows/repeatmasking from 0.1 to 0.2 --- workflows/repeatmasking/CHANGELOG.md | 5 ++ .../repeatmasking/RepeatMasking-Workflow.ga | 49 +++++++++++-------- 2 files changed, 33 insertions(+), 21 deletions(-) diff --git a/workflows/repeatmasking/CHANGELOG.md b/workflows/repeatmasking/CHANGELOG.md index 26add980d9..c603bf3dc1 100644 --- a/workflows/repeatmasking/CHANGELOG.md +++ b/workflows/repeatmasking/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.2] 2024-09-24 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.4+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.5+galaxy0` + ## [0.1] Initial version of the RepeatMasking workflow for genomic sequencing data. \ No newline at end of file diff --git a/workflows/repeatmasking/RepeatMasking-Workflow.ga b/workflows/repeatmasking/RepeatMasking-Workflow.ga index 2ebbefa8a9..22c6b0515d 100644 --- a/workflows/repeatmasking/RepeatMasking-Workflow.ga +++ b/workflows/repeatmasking/RepeatMasking-Workflow.ga @@ -3,7 +3,7 @@ "annotation": "", "format-version": "0.1", "license": "MIT", - "release": "0.1", + "release": "0.2", "name": "Repeat masking with RepeatModeler and RepeatMasker", "creator": [ { @@ -21,7 +21,7 @@ "input_connections": {}, "inputs": [ { - "description": "Apply repeat masking to this fasta file", + "description": "", "name": "input" } ], @@ -29,8 +29,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 10, - "top": 10 + "left": 0, + "top": 0 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", @@ -42,7 +42,7 @@ }, "1": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.4+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.5+galaxy0", "errors": null, "id": 1, "input_connections": { @@ -65,30 +65,32 @@ } ], "position": { - "left": 230, - "top": 10 + "left": 220, + "top": 0 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.4+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.5+galaxy0", "tool_shed_repository": { - "changeset_revision": "8661b2607b7e", + "changeset_revision": "4a172d211285", "name": "repeatmodeler", "owner": "csbl", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input_file\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0.4+galaxy1", + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.0.5+galaxy0", "type": "tool", "uuid": "9312ba36-4275-4d40-8ba6-95eea1b23b11", "when": null, "workflow_outputs": [ { + "label": "RepeatModeler consensus sequences", "output_name": "sequences", - "label": "RepeatModeler consensus sequences" + "uuid": "c99eb0e7-6470-4f85-aaa1-29abc7ec49b7" }, { + "label": "RepeatModeler seeds alignments", "output_name": "seeds", - "label": "RepeatModeler seeds alignments" + "uuid": "e2223ce1-9fcd-4a03-abad-9854417143f2" } ] }, @@ -129,8 +131,8 @@ } ], "position": { - "left": 450, - "top": 10 + "left": 440, + "top": 0 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0", @@ -140,31 +142,36 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"is_only\": false, \"is_clip\": false, \"no_is\": false, \"rodspec\": false, \"primspec\": false, \"nolow\": false, \"noint\": false, \"norna\": false, \"alu\": false, \"div\": false, \"search_speed\": \"\", \"frag\": \"40000\", \"gc\": null, \"gccalc\": false, \"nocut\": false, \"xout\": false, \"keep_alignments\": false, \"invert_alignments\": false, \"poly\": false}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"excln\": true, \"gff\": true, \"input_fasta\": null, \"repeat_source\": {\"source_type\": \"dfam\", \"__current_case__\": 0, \"species_source\": {\"species_from_list\": \"no\", \"__current_case__\": 1, \"species_name\": \"\"}}, \"xsmall\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"is_only\": false, \"is_clip\": false, \"no_is\": false, \"rodspec\": false, \"primspec\": false, \"nolow\": false, \"noint\": false, \"norna\": false, \"alu\": false, \"div\": false, \"search_speed\": \"\", \"frag\": \"40000\", \"gc\": null, \"gccalc\": false, \"nocut\": false, \"xout\": false, \"keep_alignments\": false, \"invert_alignments\": false, \"poly\": false}, \"chromInfo\": \"/shared/ifbstor1/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"excln\": true, \"gff\": true, \"input_fasta\": {\"__class__\": \"ConnectedValue\"}, \"repeat_source\": {\"source_type\": \"dfam\", \"__current_case__\": 0, \"species_source\": {\"species_from_list\": \"no\", \"__current_case__\": 1, \"species_name\": \"\"}}, \"xsmall\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "4.1.5+galaxy0", "type": "tool", "uuid": "e6c8e6a1-efe8-4291-b12b-5fdb3795b6ca", "when": null, "workflow_outputs": [ { + "label": "RepeatMasker masked genome", "output_name": "output_masked_genome", - "label": "RepeatMasker masked genome" + "uuid": "2e143b9b-038d-45f0-b3bb-232e484b3f42" }, { + "label": "RepeatMasker output log", "output_name": "output_log", - "label": "RepeatMasker output log" + "uuid": "0bea14a2-4d6c-4ffc-878d-f9c5a441ea94" }, { + "label": "RepeatMasker repeat statistics", "output_name": "output_table", - "label": "RepeatMasker repeat statistics" + "uuid": "81b6ded1-f317-46e2-93b5-69a5a529f4fd" }, { + "label": "RepeatMasker repeat catalog", "output_name": "output_repeat_catalog", - "label": "RepeatMasker repeat catalog" + "uuid": "d591f44a-b608-4118-a7f4-cb692d2cce4e" }, { + "label": "RepeatMasker repeat annotation", "output_name": "output_gff", - "label": "RepeatMasker repeat annotation" + "uuid": "6c469577-3f6a-4d46-9a3e-8e7459038cb0" } ] }