Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 7 additions & 0 deletions workflows/microbiome/binning-evaluation/CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -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
Expand Down
36 changes: 18 additions & 18 deletions workflows/microbiome/binning-evaluation/MAGs-binning-evaluation.ga
Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand All @@ -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,
Expand Down Expand Up @@ -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": {
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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": {
Expand All @@ -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,
Expand Down Expand Up @@ -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": {
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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"
}
Loading