From abd73e76bab543b948f2447834d7141ec20937ad Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 20 Jul 2026 09:04:03 +0000 Subject: [PATCH 1/3] Updating workflows/microbiome/metagenomic-raw-reads-amr-analysis from 1.2 to 1.3 --- .../CHANGELOG.md | 5 +++++ .../metagenomic-raw-reads-amr-analysis.ga | 14 +++++++------- 2 files changed, 12 insertions(+), 7 deletions(-) diff --git a/workflows/microbiome/metagenomic-raw-reads-amr-analysis/CHANGELOG.md b/workflows/microbiome/metagenomic-raw-reads-amr-analysis/CHANGELOG.md index eeedefab7a..ee36650f71 100644 --- a/workflows/microbiome/metagenomic-raw-reads-amr-analysis/CHANGELOG.md +++ b/workflows/microbiome/metagenomic-raw-reads-amr-analysis/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [1.3] - 2026-07-20 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy2` + ## [1.2] - 2026-06-22 ### Automatic update diff --git a/workflows/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis.ga b/workflows/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis.ga index 2e66c5b927..57b6e0dc9b 100644 --- a/workflows/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis.ga +++ b/workflows/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis.ga @@ -1602,7 +1602,7 @@ }, "28": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy2", "errors": null, "id": 28, "input_connections": { @@ -1650,16 +1650,16 @@ "output_name": "html_report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy2", "tool_shed_repository": { - "changeset_revision": "fac2260bc88a", + "changeset_revision": "0559e0711094", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"image_content_input\": {\"__class__\": \"RuntimeValue\"}, \"png_plots\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 54, \"plot_type\": \"table\", \"section_name\": \"ARGs detected by Groot and normalized with argNorm\", \"title\": null, \"description\": null, \"xlab\": null, \"ylab\": null, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 54, \"plot_type\": \"table\", \"section_name\": \"ARGs detected by DeepARG\", \"title\": null, \"description\": null, \"xlab\": null, \"ylab\": null, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"sylphtax\", \"__current_case__\": 30, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"title\": \"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"image_content_input\": {\"__class__\": \"RuntimeValue\"}, \"png_plots\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 55, \"plot_type\": \"table\", \"section_name\": \"ARGs detected by Groot and normalized with argNorm\", \"title\": null, \"description\": null, \"xlab\": null, \"ylab\": null, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"custom_content\", \"__current_case__\": 55, \"plot_type\": \"table\", \"section_name\": \"ARGs detected by DeepARG\", \"title\": null, \"description\": null, \"xlab\": null, \"ylab\": null, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"sylphtax\", \"__current_case__\": 30, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"title\": \"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "1.35+galaxy1", + "tool_version": "1.35+galaxy2", "type": "tool", "uuid": "e9799c84-007c-4980-9acd-9a5a619aa19d", "when": null, @@ -1680,7 +1680,7 @@ "ABRomics", "short-reads" ], - "uuid": "6223b940-5cdf-4259-80b2-6439f6c952b7", + "uuid": "a825fb98-ad98-436b-9ce5-a264edf93987", "version": 1, - "release": "1.2" + "release": "1.3" } \ No newline at end of file From 9707e5840f9fdf41e04253726b6fe1069633252a Mon Sep 17 00:00:00 2001 From: Hugo Lefeuvre <161316836+hugolefeuvre@users.noreply.github.com> Date: Mon, 20 Jul 2026 11:27:15 +0200 Subject: [PATCH 2/3] Update release version to 1.2.1 --- .../metagenomic-raw-reads-amr-analysis.ga | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis.ga b/workflows/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis.ga index 57b6e0dc9b..fd54a10264 100644 --- a/workflows/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis.ga +++ b/workflows/microbiome/metagenomic-raw-reads-amr-analysis/metagenomic-raw-reads-amr-analysis.ga @@ -1682,5 +1682,5 @@ ], "uuid": "a825fb98-ad98-436b-9ce5-a264edf93987", "version": 1, - "release": "1.3" -} \ No newline at end of file + "release": "1.2.1" +} From 17072ae71879b56afc192ddbfe91f00c8d6f41b7 Mon Sep 17 00:00:00 2001 From: Hugo Lefeuvre <161316836+hugolefeuvre@users.noreply.github.com> Date: Mon, 20 Jul 2026 11:27:39 +0200 Subject: [PATCH 3/3] Change version from 1.3 to 1.2.1 in CHANGELOG.md Updated version number and date for the changelog. --- .../microbiome/metagenomic-raw-reads-amr-analysis/CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/microbiome/metagenomic-raw-reads-amr-analysis/CHANGELOG.md b/workflows/microbiome/metagenomic-raw-reads-amr-analysis/CHANGELOG.md index ee36650f71..51fec3d4fa 100644 --- a/workflows/microbiome/metagenomic-raw-reads-amr-analysis/CHANGELOG.md +++ b/workflows/microbiome/metagenomic-raw-reads-amr-analysis/CHANGELOG.md @@ -1,6 +1,6 @@ # Changelog -## [1.3] - 2026-07-20 +## [1.2.1] - 2026-07-20 ### Automatic update - `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.35+galaxy2`