From 23c8beb712e8584132aee0ea68ca274f4f1fe33f Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 3 Feb 2025 05:35:29 +0000 Subject: [PATCH 1/2] Updating workflows/transcriptomics/rnaseq-de from 0.2 to 0.3 --- workflows/transcriptomics/rnaseq-de/CHANGELOG.md | 5 +++++ .../rnaseq-de/rnaseq-de-filtering-plotting.ga | 12 ++++++------ 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-de/CHANGELOG.md b/workflows/transcriptomics/rnaseq-de/CHANGELOG.md index 961f2d8da2..230af45858 100644 --- a/workflows/transcriptomics/rnaseq-de/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-de/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.3] 2025-02-03 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.7` + ## [0.2] 2024-11-18 ### Automatic update diff --git a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga index 9aa8986938..e5751f703d 100644 --- a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga +++ b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga @@ -11,7 +11,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.2", + "release": "0.3", "name": "RNAseq_DE_filtering_plotting", "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" @@ -778,7 +778,7 @@ }, "18": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.7", "errors": null, "id": 18, "input_connections": { @@ -809,15 +809,15 @@ "top": 957.2308087191843 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.7", "tool_shed_repository": { - "changeset_revision": "2f557f6abbfb", + "changeset_revision": "5e08a1e22dbc", "name": "volcanoplot", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"fdr_col\": \"7\", \"header\": \"yes\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"label_col\": \"13\", \"labels\": {\"label_select\": \"signif\", \"__current_case__\": 0, \"top_num\": \"10\"}, \"lfc_col\": \"3\", \"lfc_thresh\": {\"__class__\": \"ConnectedValue\"}, \"out_options\": {\"rscript_out\": false}, \"plot_options\": {\"boxes\": false, \"title\": null, \"xlab\": null, \"ylab\": null, \"xmin\": null, \"xmax\": null, \"ymax\": null, \"legend\": null, \"legend_labs\": \"Down,Not Sig,Up\"}, \"pval_col\": \"6\", \"signif_thresh\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.0.6", + "tool_state": "{\"fdr_col\": \"7\", \"header\": \"yes\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"label_col\": \"13\", \"labels\": {\"label_select\": \"signif\", \"__current_case__\": 0, \"top_num\": \"10\"}, \"lfc_col\": \"3\", \"lfc_thresh\": {\"__class__\": \"ConnectedValue\"}, \"out_options\": {\"rscript_out\": false}, \"plot_options\": {\"boxes\": false, \"title\": null, \"xlab\": null, \"ylab\": null, \"xmin\": null, \"xmax\": null, \"ymax\": null, \"legend\": null, \"legend_labs\": \"Down,Not Sig,Up\"}, \"pval_col\": \"6\", \"shape_or_facet\": null, \"signif_thresh\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.0.7", "type": "tool", "uuid": "cb314a3d-0b05-4d45-a961-591d59b3852b", "when": null, From ca381b38e9a599bcf1e4c954fa42a5eab688a7de Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 6 Feb 2025 11:13:04 +0100 Subject: [PATCH 2/2] add new shape_col param --- .../transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga index e5751f703d..50c5d6805f 100644 --- a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga +++ b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga @@ -816,7 +816,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"fdr_col\": \"7\", \"header\": \"yes\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"label_col\": \"13\", \"labels\": {\"label_select\": \"signif\", \"__current_case__\": 0, \"top_num\": \"10\"}, \"lfc_col\": \"3\", \"lfc_thresh\": {\"__class__\": \"ConnectedValue\"}, \"out_options\": {\"rscript_out\": false}, \"plot_options\": {\"boxes\": false, \"title\": null, \"xlab\": null, \"ylab\": null, \"xmin\": null, \"xmax\": null, \"ymax\": null, \"legend\": null, \"legend_labs\": \"Down,Not Sig,Up\"}, \"pval_col\": \"6\", \"shape_or_facet\": null, \"signif_thresh\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"fdr_col\": \"7\", \"header\": \"yes\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"label_col\": \"13\", \"labels\": {\"label_select\": \"signif\", \"__current_case__\": 0, \"top_num\": \"10\"}, \"lfc_col\": \"3\", \"lfc_thresh\": {\"__class__\": \"ConnectedValue\"}, \"out_options\": {\"rscript_out\": false}, \"plot_options\": {\"boxes\": false, \"title\": null, \"xlab\": null, \"ylab\": null, \"xmin\": null, \"xmax\": null, \"ymax\": null, \"legend\": null, \"legend_labs\": \"Down,Not Sig,Up\"}, \"pval_col\": \"6\", \"shape_col\": \"\", \"shape_or_facet\": null, \"signif_thresh\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_version": "0.0.7", "type": "tool", "uuid": "cb314a3d-0b05-4d45-a961-591d59b3852b", @@ -1131,4 +1131,4 @@ ], "uuid": "15d188a7-b028-4cf7-bb5d-13858e1f6e78", "version": 15 -} \ No newline at end of file +}