From 527b9131bb74ec30bb69fa2d250fdb2193f6441c Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 24 Nov 2025 08:14:15 +0000 Subject: [PATCH] Updating workflows/virology/pox-virus-amplicon from 0.4 to 0.5 --- .../virology/pox-virus-amplicon/CHANGELOG.md | 9 ++ .../pox-virus-half-genome.ga | 98 +++++++++---------- 2 files changed, 58 insertions(+), 49 deletions(-) diff --git a/workflows/virology/pox-virus-amplicon/CHANGELOG.md b/workflows/virology/pox-virus-amplicon/CHANGELOG.md index 8cb0719b05..aaf8604d91 100644 --- a/workflows/virology/pox-virus-amplicon/CHANGELOG.md +++ b/workflows/virology/pox-virus-amplicon/CHANGELOG.md @@ -1,5 +1,14 @@ # Changelog +## [0.5] - 2025-11-24 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.21+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.22+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.7` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.8` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy4` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.21+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.22+galaxy1` + ## [0.4] - 2025-10-08 ### Automatic update diff --git a/workflows/virology/pox-virus-amplicon/pox-virus-half-genome.ga b/workflows/virology/pox-virus-amplicon/pox-virus-half-genome.ga index ec9070d962..87f3b6ceb3 100644 --- a/workflows/virology/pox-virus-amplicon/pox-virus-half-genome.ga +++ b/workflows/virology/pox-virus-amplicon/pox-virus-half-genome.ga @@ -398,7 +398,7 @@ }, "11": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy3", "errors": null, "id": 11, "input_connections": { @@ -463,15 +463,15 @@ "output_name": "report_html" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy3", "tool_shed_repository": { - "changeset_revision": "1c183b0a6cfd", + "changeset_revision": "f875da9d433c", "name": "fastp", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_front_select\": {\"cut_front\": \"\", \"__current_case__\": 1}, \"cut_tail_select\": {\"cut_tail\": \"\", \"__current_case__\": 1}, \"cut_right_select\": {\"cut_right\": \"\", \"__current_case__\": 1}}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 1, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"merge_reads\": {\"merge\": \"\", \"__current_case__\": 1}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\", \"detect_adapter_for_pe\": false}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - 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