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Update for version 1.1
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iwc-workflows-bot committed Jun 24, 2024
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5 changes: 5 additions & 0 deletions CHANGELOG.md
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# Changelog

## [1.1] 2024-06-24

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0`

## [1.0] - 14-06-2024

- First release
39 changes: 27 additions & 12 deletions bacterial_genome_annotation.ga
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"alternateName": "pimarin",
"class": "Person",
"identifier": "https://orcid.org/0000-0002-8304-138X",
"name": "Pierre Marin",
"alternateName": "pimarin"
"name": "Pierre Marin"
},
{
"alternateName": "clsiguret",
"class": "Person",
"identifier": "https://orcid.org/0009-0005-6140-0379",
"name": "Clea Siguret",
"alternateName": "clsiguret"
"name": "Clea Siguret"
}
],
"format-version": "0.1",
"license": "GPL-3.0-or-later",
"release": "1.0",
"release": "1.1",
"name": "bacterial_genome_annotation",
"steps": {
"0": {
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"top": 734.3939210886799
},
"tool_id": null,
"tool_state": "{\"default\": \"plasmidfinder_81c11f4_2023_12_04\", \"restrictions\": [\"plasmidfinder_314d85f_2023_03_17\",\"81c11f4_2023_12_04/\"], \"parameter_type\": \"text\", \"optional\": true}",
"tool_state": "{\"default\": \"plasmidfinder_81c11f4_2023_12_04\", \"restrictions\": [\"plasmidfinder_314d85f_2023_03_17\", \"81c11f4_2023_12_04/\"], \"parameter_type\": \"text\", \"optional\": true}",
"tool_version": null,
"type": "parameter_input",
"uuid": "66c11ad1-7cd5-40b7-b97f-8d15cc097dd9",
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},
"5": {
"annotation": "genomic_annotation_integron",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.3+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
"errors": null,
"id": 5,
"input_connections": {
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"output_name": "summary"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.3+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.5+galaxy0",
"tool_shed_repository": {
"changeset_revision": "392f100eebcd",
"changeset_revision": "bfd290fe1588",
"name": "integron_finder",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"gbk\": false, \"local_max\": true, \"no_logfile\": false, \"pdf\": false, \"promoter_attI\": true, \"sequence\": {\"__class__\": \"ConnectedValue\"}, \"settings\": {\"attc_settings\": {\"dist_thresh\": \"4000\", \"calin_threshold\": \"2\", \"max_attc_size\": \"200\", \"min_attc_size\": \"40\", \"keep_palindromes\": false, \"covar_matrix\": {\"__class__\": \"RuntimeValue\"}}, \"protein_settings\": {\"no_proteins\": false, \"union_integrases\": false, \"func_annot\": false}}, \"topology_file\": {\"__class__\": \"RuntimeValue\"}, \"type_replicon\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.0.3+galaxy0",
"tool_version": "2.0.5+galaxy0",
"type": "tool",
"uuid": "0f39c064-cac7-4ee7-9f37-94b7717a033e",
"when": null,
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"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool PlasmidFinder",
"name": "input"
},
{
"description": "runtime parameter for tool PlasmidFinder",
"name": "input"
}
],
"label": "genomic_annotation_plasmid_plasmidfinder",
"name": "PlasmidFinder",
"outputs": [
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"description": "runtime parameter for tool Bakta",
"name": "annotation"
},
{
"description": "runtime parameter for tool Bakta",
"name": "input_option"
},
{
"description": "runtime parameter for tool Bakta",
"name": "input_option"
},
{
"description": "runtime parameter for tool Bakta",
"name": "input_option"
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"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"annotation\": {\"complete\": false, \"prodigal\": {\"__class__\": \"RuntimeValue\"}, \"translation_table\": \"11\", \"keep_contig_headers\": false, \"replicons\": {\"__class__\": \"RuntimeValue\"}, \"compliant\": false, \"proteins\": {\"__class__\": \"RuntimeValue\"}, \"meta\": false, \"regions\": {\"__class__\": \"RuntimeValue\"}}, \"input_option\": {\"input_file\": {\"__class__\": \"RuntimeValue\"}, \"min_contig_length\": null, \"bakta_db_select\": {\"__class__\": \"ConnectedValue\"}, \"amrfinder_db_select\": {\"__class__\": \"ConnectedValue\"}}, \"organism\": {\"genus\": null, \"species\": null, \"strain\": null, \"plasmid\": null}, \"output_files\": {\"output_selection\": [\"file_tsv\", \"file_gff3\", \"file_ffn\", \"file_plot\", \"file_gbff\", \"file_embl\", \"file_fna\", \"file_faa\", \"hypo_tsv\", \"hypo_fa\", \"file_json\", \"sum_txt\"]}, \"workflow\": {\"skip_analysis\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"annotation\": {\"complete\": false, \"prodigal\": {\"__class__\": \"RuntimeValue\"}, \"translation_table\": \"11\", \"keep_contig_headers\": false, \"replicons\": {\"__class__\": \"RuntimeValue\"}, \"compliant\": false, \"proteins\": {\"__class__\": \"RuntimeValue\"}, \"meta\": false, \"regions\": {\"__class__\": \"RuntimeValue\"}}, \"input_option\": {\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"min_contig_length\": null, \"bakta_db_select\": {\"__class__\": \"ConnectedValue\"}, \"amrfinder_db_select\": {\"__class__\": \"ConnectedValue\"}}, \"organism\": {\"genus\": null, \"species\": null, \"strain\": null, \"plasmid\": null}, \"output_files\": {\"output_selection\": [\"file_tsv\", \"file_gff3\", \"file_ffn\", \"file_plot\", \"file_gbff\", \"file_embl\", \"file_fna\", \"file_faa\", \"hypo_tsv\", \"hypo_fa\", \"file_json\", \"sum_txt\"]}, \"workflow\": {\"skip_analysis\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.9.3+galaxy0",
"type": "tool",
"uuid": "0a32dcad-f456-460e-9e6f-9e306a8fd515",
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8 changes: 4 additions & 4 deletions ro-crate-metadata.json
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{
"@id": "./",
"@type": "Dataset",
"datePublished": "2024-06-19T11:29:55.009783",
"datePublished": "2024-06-24T12:34:13.326994",
"hasPart": [
{
"@id": "bacterial_genome_annotation.ga"
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],
"creator": [
{
"@id": "#9ef2fbf5-8de8-43ef-a899-c9e877de0e7b"
"@id": "#fd061885-8231-4704-8f27-4b6d64911256"
},
{
"@id": "https://www.abromics.fr/"
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"@id": "#galaxy"
},
"url": "https://github.com/iwc-workflows/bacterial_genome_annotation",
"version": "1.0"
"version": "1.1"
},
{
"@id": "#galaxy",
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"version": "v19_09"
},
{
"@id": "#9ef2fbf5-8de8-43ef-a899-c9e877de0e7b",
"@id": "#fd061885-8231-4704-8f27-4b6d64911256",
"@type": "Person",
"name": "ABRomics"
},
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