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Quality and contamination control workflow update from 1.1.1 to 1.1.2 (…
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…#520)

* Updating workflows/genome-assembly/quality-and-contamination-control from 1.1.1 to 1.1.2

* Add Recentrifuge database in input parameter + change tool versions for ToolDistillator

* Update Changelog

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Co-authored-by: planemo-autoupdate <[email protected]>
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@clsiguret
clsiguret and planemo-autoupdate authored Sep 18, 2024
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10 changes: 10 additions & 0 deletions workflows/genome-assembly/quality-and-contamination-control/CHANGELOG.md
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# Changelog

## [1.1.2] 2024-08-05

### Manual update

- Updated the tool versions manually in the ToolDistillator parameters

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.0+galaxy0`
- `toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.1+galaxy0`

## [1.1.1] 2024-07-08

### Automatic update
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22 changes: 11 additions & 11 deletions ...ws/genome-assembly/quality-and-contamination-control/quality_and_contamination_control.ga
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],
"format-version": "0.1",
"license": "GPL-3.0-or-later",
"release": "1.1.1",
"release": "1.1.2",
"name": "Quality and Contamination Control For Genome Assembly",
"steps": {
"0": {
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"top": 454.91066885428484
},
"tool_id": null,
"tool_state": "{\"default\": \"ncbi-2015-10-05\", \"restrictions\": [\"ncbi-2015-10-05\"], \"parameter_type\": \"text\", \"optional\": true}",
"tool_state": "{\"default\": \"ncbi-2015-10-05\", \"restrictions\": [\"ncbi-2015-10-05\", \"2020-12-03\", \"2022-03-08\", \"2024-06-05\"], \"parameter_type\": \"text\", \"optional\": true}",
"tool_version": null,
"type": "parameter_input",
"uuid": "daac0634-bcf4-4fdd-bcd2-67247f5afdd0",
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},
"6": {
"annotation": "bracken_abundance_estimation",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.0+galaxy0",
"errors": null,
"id": 6,
"input_connections": {
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"output_name": "report"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.0+galaxy0",
"tool_shed_repository": {
"changeset_revision": "1d4bd12f01cf",
"changeset_revision": "0c7b6eb7e752",
"name": "bracken",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_distr\": {\"__class__\": \"ConnectedValue\"}, \"level\": \"S\", \"logfile_output\": false, \"out_report\": true, \"threshold\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.9+galaxy0",
"tool_version": "3.0+galaxy0",
"type": "tool",
"uuid": "e088cdc6-d79b-453c-8787-6d4b7004312a",
"when": null,
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},
"7": {
"annotation": "recentrifuge_taxonomy_visualization",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.0+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.1+galaxy0",
"errors": null,
"id": 7,
"input_connections": {
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"output_name": "stat_tsv"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.0+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.1+galaxy0",
"tool_shed_repository": {
"changeset_revision": "76bf12b928f4",
"changeset_revision": "d4fbfd31696c",
"name": "recentrifuge",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"advanced_option\": {\"controls\": \"0\", \"scoring\": null, \"minscore_value\": \"0\", \"mintaxa\": \"0\", \"exclude_taxa_name\": null, \"include_taxa_name\": null, \"avoidcross\": false}, \"database\": {\"database_name\": {\"__class__\": \"ConnectedValue\"}}, \"file_type\": {\"filetype\": \"kraken\", \"__current_case__\": 3}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"more_advanced_option\": {\"ctrlminscore\": \"0\", \"ctrlmintaxa\": \"0\", \"summary\": \"ADD\", \"takeoutroot\": false, \"nokollapse\": false, \"strain\": true, \"sequential\": false}, \"output_option\": {\"extra\": \"TSV\", \"nohtml\": false, \"no_logfile\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.14.0+galaxy0",
"tool_version": "1.14.1+galaxy0",
"type": "tool",
"uuid": "2db5d20e-62c7-43ad-b21f-e9992c77faa1",
"when": null,
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"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"fastp\", \"__current_case__\": 6, \"input\": {\"__class__\": \"ConnectedValue\"}, \"trimmed_forward_R1_path\": {\"__class__\": \"ConnectedValue\"}, \"trimmed_reverse_R2_path\": {\"__class__\": \"ConnectedValue\"}, \"html_report_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"0.23.2\", \"reference_database_version\": null}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"kraken2\", \"__current_case__\": 12, \"input\": {\"__class__\": \"ConnectedValue\"}, \"seq_classification_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.1.1\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"bracken\", \"__current_case__\": 4, \"input\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.8\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}, \"kraken_report_path\": {\"__class__\": \"ConnectedValue\"}, \"threshold\": null, \"read_len\": \"100\", \"level\": \"S\"}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"recentrifuge\", \"__current_case__\": 17, \"input\": {\"__class__\": \"ConnectedValue\"}, \"rcf_stat_path\": {\"__class__\": \"ConnectedValue\"}, \"rcf_html_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.12.1\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"log\": false, \"tool_section\": {\"tools\": [{\"__index__\": 0, \"select_tool\": {\"tool_list\": \"fastp\", \"__current_case__\": 6, \"input\": {\"__class__\": \"ConnectedValue\"}, \"trimmed_forward_R1_path\": {\"__class__\": \"ConnectedValue\"}, \"trimmed_reverse_R2_path\": {\"__class__\": \"ConnectedValue\"}, \"html_report_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"0.23.4\", \"reference_database_version\": null}}, {\"__index__\": 1, \"select_tool\": {\"tool_list\": \"kraken2\", \"__current_case__\": 12, \"input\": {\"__class__\": \"ConnectedValue\"}, \"seq_classification_file_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"2.1.3\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"select_tool\": {\"tool_list\": \"bracken\", \"__current_case__\": 4, \"input\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"3.0\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}, \"kraken_report_path\": {\"__class__\": \"ConnectedValue\"}, \"threshold\": null, \"read_len\": \"100\", \"level\": \"S\"}}, {\"__index__\": 3, \"select_tool\": {\"tool_list\": \"recentrifuge\", \"__current_case__\": 17, \"input\": {\"__class__\": \"ConnectedValue\"}, \"rcf_stat_path\": {\"__class__\": \"ConnectedValue\"}, \"rcf_html_path\": {\"__class__\": \"ConnectedValue\"}, \"analysis_software_version\": \"1.14.1\", \"reference_database_version\": {\"__class__\": \"ConnectedValue\"}}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "0.9+galaxy0",
"type": "tool",
"uuid": "b88b0ffe-f660-43ea-b00a-40ca0087f83f",
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