From 703fd1e74ed2e695373553c74a93ec0b4b1f8c94 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 20 Apr 2026 08:01:32 +0000 Subject: [PATCH] Updating workflows/microbiome/binning-evaluation from 1.1 to 1.2 --- .../binning-evaluation/CHANGELOG.md | 7 ++++ .../MAGs-binning-evaluation.ga | 36 +++++++++---------- 2 files changed, 25 insertions(+), 18 deletions(-) diff --git a/workflows/microbiome/binning-evaluation/CHANGELOG.md b/workflows/microbiome/binning-evaluation/CHANGELOG.md index ec63c50b28..e3a709c877 100644 --- a/workflows/microbiome/binning-evaluation/CHANGELOG.md +++ b/workflows/microbiome/binning-evaluation/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +## [1.2] - 2026-04-20 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3` +- `toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy1` + ## [1.1] - 2026-03-09 ### Automatic update diff --git a/workflows/microbiome/binning-evaluation/MAGs-binning-evaluation.ga b/workflows/microbiome/binning-evaluation/MAGs-binning-evaluation.ga index dfc9cca000..0a9caa574c 100644 --- a/workflows/microbiome/binning-evaluation/MAGs-binning-evaluation.ga +++ b/workflows/microbiome/binning-evaluation/MAGs-binning-evaluation.ga @@ -990,7 +990,7 @@ }, "30": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3", "errors": null, "id": 30, "input_connections": { @@ -1013,16 +1013,16 @@ "top": 270 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3", "tool_shed_repository": { - "changeset_revision": "d3c07d270a50", + "changeset_revision": "3e27acfa4830", "name": "collection_element_identifiers", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_collection\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "0.0.2", + "tool_version": "0.0.3", "type": "tool", "uuid": "561188b3-dad5-4434-8872-40eb96e2f71d", "when": null, @@ -1363,7 +1363,7 @@ }, "38": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy1", "errors": null, "id": 38, "input_connections": { @@ -1391,16 +1391,16 @@ "top": 1750 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/metabat2_jgi_summarize_bam_contig_depths/metabat2_jgi_summarize_bam_contig_depths/2.17+galaxy1", "tool_shed_repository": { - "changeset_revision": "00e3b4ef7e0c", + "changeset_revision": "6b51b29c0147", "name": "metabat2_jgi_summarize_bam_contig_depths", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"advanced\": {\"percentIdentity\": \"97\", \"output_paired_contigs\": false, \"noIntraDepthVariance\": false, \"showDepth\": false, \"minMapQual\": \"0\", \"weightMapQual\": \"0.0\", \"includeEdgeBases\": false, \"maxEdgeBases\": \"75\"}, \"bam_indiv_input|__identifier__\": \"ERR2231567.fastqsanger\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"mode\": {\"type\": \"individual\", \"__current_case__\": 0, \"bam_indiv_input\": {\"__class__\": \"ConnectedValue\"}, \"use_reference_cond\": {\"use_reference\": \"no\", \"__current_case__\": 0}}, \"shredding\": {\"shredLength\": \"16000\", \"shredDepth\": \"5\", \"minContigLength\": \"1\", \"minContigDepth\": \"0.0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "2.17+galaxy0", + "tool_version": "2.17+galaxy1", "type": "tool", "uuid": "46bcb6d3-507d-4d30-a4b0-198683f8e314", "when": null, @@ -1512,7 +1512,7 @@ }, "40": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3", "errors": null, "id": 40, "input_connections": { @@ -1535,16 +1535,16 @@ "top": 760 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3", "tool_shed_repository": { - "changeset_revision": "d3c07d270a50", + "changeset_revision": "3e27acfa4830", "name": "collection_element_identifiers", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input_collection\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "0.0.2", + "tool_version": "0.0.3", "type": "tool", "uuid": "d321ccdf-c1ef-497e-a2f7-6e7ac36ffc50", "when": null, @@ -1661,7 +1661,7 @@ }, "42": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy1", "errors": null, "id": 42, "input_connections": { @@ -1784,16 +1784,16 @@ "output_name": "bins" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/metabat2/metabat2/2.17+galaxy1", "tool_shed_repository": { - "changeset_revision": "f375b4f6ef57", + "changeset_revision": "a040f2dc705c", "name": "metabat2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced\": {\"base_coverage_depth_cond\": {\"base_coverage_depth\": \"yes\", \"__current_case__\": 1, \"abdFile\": {\"__class__\": \"ConnectedValue\"}, \"cvExt\": {\"__class__\": \"RuntimeValue\"}}, \"minContig\": {\"__class__\": \"ConnectedValue\"}, \"maxP\": {\"__class__\": \"ConnectedValue\"}, \"minS\": {\"__class__\": \"ConnectedValue\"}, \"maxEdges\": {\"__class__\": \"ConnectedValue\"}, \"pTNF\": {\"__class__\": \"ConnectedValue\"}, \"noAdd\": false, \"minCV\": {\"__class__\": \"ConnectedValue\"}, \"minCVSum\": {\"__class__\": \"ConnectedValue\"}, \"seed\": {\"__class__\": \"ConnectedValue\"}}, \"inFile\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"minClsSize\": \"200000\", \"onlyLabel\": false, \"saveCls\": false, \"extra_outputs\": [\"lowDepth\", \"tooShort\", \"unbinned\", \"log\"]}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", "tool_uuid": null, - "tool_version": "2.17+galaxy0", + "tool_version": "2.17+galaxy1", "type": "tool", "uuid": "c1caaa1f-537c-4d93-b5b2-e6299fb49b1d", "when": null, @@ -3567,7 +3567,7 @@ "tags": [ "name:MAGs" ], - "uuid": "73874fb0-bdec-472d-a056-97d6361e864a", + "uuid": "31c4f3a0-6fb9-4675-8f5c-3d6b23a47fb2", "version": 1, - "release": "1.1" + "release": "1.2" } \ No newline at end of file