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Updating workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0 from 0.2.2 to 0.2.3 #1211

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Updating workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0 from 0.2.2 to 0.2.3 #1211

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5 changes: 5 additions & 0 deletions workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
# Changelog

## [0.2.3] - 2026-06-15

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy2`

## [0.2.2] - 2025-08-25

### Changes
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59 changes: 43 additions & 16 deletions workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0.ga
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Expand Up @@ -15,7 +15,6 @@
],
"format-version": "0.1",
"license": "CC-BY-4.0",
"release": "0.2.2",
"name": "Mitogenome Assembly VGP0",
"report": {
"markdown": "Species : \n\n```galaxy\nhistory_dataset_embedded(output=\"Species Name for report\")\n```\n\nAssembly:\n\n\n```galaxy\nhistory_dataset_embedded(output=\"Assembly Name for report\")\n```\n\n\n## Annotation\n\n```galaxy\nhistory_dataset_as_image(output=\"Mitogenome annotation: Image\")\n```\n\n## Coverage\n\n\n\r\n```galaxy\nhistory_dataset_as_image(output=\"Mitogenome coverage: Image\")\n```\r\n\n\n## Contigs Stats\n\n\n```galaxy\nhistory_dataset_as_table(output=\"Mitogenome: Contigs Statistics\")\n```\n"
Expand Down Expand Up @@ -107,7 +106,7 @@
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"type": "data_collection_input",
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Expand Down Expand Up @@ -219,6 +218,7 @@
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Expand Down Expand Up @@ -270,6 +270,7 @@
"tool_shed": "toolshed.g2.bx.psu.edu"
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Expand All @@ -284,7 +285,7 @@
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Expand All @@ -297,7 +298,16 @@
"output_name": "output"
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"name": "MitoHiFi",
"outputs": [
Expand All @@ -315,23 +325,24 @@
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"tool_version": "3.2.3+galaxy0",
"tool_state": "{\"operation_mode\": {\"command\": \"find_reference\", \"__current_case__\": 0, \"species\": {\"__class__\": \"ConnectedValue\"}, \"email\": {\"__class__\": \"ConnectedValue\"}, \"organelle_type\": \"mitochondrion\", \"ncbi_api_key\": \"\", \"min_length\": \"15000\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
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Expand All @@ -352,7 +363,20 @@
"output_name": "genbank_reference"
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"name": "MitoHiFi",
"outputs": [
Expand Down Expand Up @@ -471,15 +495,16 @@
"output_name": "mitogenome_genbank"
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"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/mitohifi/mitohifi/3.2.3+galaxy2",
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"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
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"tool_state": "{\"operation_mode\": {\"command\": \"mitohifi\", \"__current_case__\": 1, \"input_option\": {\"input\": \"pacbio\", \"__current_case__\": 0, \"input_reads\": {\"__class__\": \"RuntimeValue\"}, \"bloom_filter\": \"0\"}, \"reference_fasta\": {\"__class__\": \"RuntimeValue\"}, \"reference_genbank\": {\"__class__\": \"RuntimeValue\"}, \"organism_selection\": \"animal\", \"genetic_code\": {\"__class__\": \"ConnectedValue\"}, \"advanced_options\": {\"query_blast\": \"70\", \"circular_size\": null, \"circular_offset\": null, \"outputs\": null}, \"output_zip\": false}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.3+galaxy0",
"tool_state": "{\"operation_mode\": {\"command\": \"mitohifi\", \"__current_case__\": 1, \"input_option\": {\"input\": \"pacbio\", \"__current_case__\": 0, \"input_reads\": {\"__class__\": \"ConnectedValue\"}, \"bloom_filter\": \"0\"}, \"reference_fasta\": {\"__class__\": \"ConnectedValue\"}, \"reference_genbank\": {\"__class__\": \"ConnectedValue\"}, \"organism_selection\": \"animal\", \"genetic_code\": {\"__class__\": \"ConnectedValue\"}, \"advanced_options\": {\"query_blast\": \"70\", \"circular_size\": null, \"circular_offset\": null, \"outputs\": null}, \"output_zip\": false}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
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"when": null,
Expand Down Expand Up @@ -554,6 +579,7 @@
"tool_shed": "toolshed.g2.bx.psu.edu"
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"tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_uuid": null,
"tool_version": "0.1.0",
"type": "tool",
"uuid": "5207adc9-f36a-42e9-8631-e01da77ac446",
Expand All @@ -571,6 +597,7 @@
"Reviewed",
"VGP"
],
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"version": 1
"uuid": "15e111b8-e41a-46a3-b8c7-a52802703c23",
"version": 1,
"release": "0.2.3"
}
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