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Updating workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 from…
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… 0.3 to 0.4
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planemo-autoupdate committed Dec 16, 2024
1 parent 7c7c341 commit 5d3ed92
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45 changes: 34 additions & 11 deletions workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9.ga
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],
"format-version": "0.1",
"license": "BSD-3-Clause",
"release": "0.3",
"release": "0.4",
"name": "Assembly-decontamination-VGP9",
"report": {
"markdown": "\n# Workflow Execution Report\n\n### Worflow ran on: \n\n```galaxy\ninvocation_time()\n```\n\n# List of contaminants\n\n\r\n```galaxy\nhistory_dataset_as_table(output=\"contaminants_table\")\n```\r\n\n\n# List of Mitochondrial scaffolds\n\r\n```galaxy\nhistory_dataset_as_table(output=\"mito_scaff_names\")\n```\r\n\n\n\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
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"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool NCBI BLAST+ dustmasker",
"name": "db_opts"
}
],
"label": "soft-masking ",
"name": "NCBI BLAST+ dustmasker",
"outputs": [
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"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"/^>/!y/atcgn/NNNNN/\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"basic\", \"__current_case__\": 0}, \"code\": \"/^>/!y/atcgn/NNNNN/\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "9.3+galaxy1",
"type": "tool",
"uuid": "5089350b-c1a9-498a-9786-9864d484f77a",
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"output_name": "output"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Kraken2",
"name": "single_paired"
}
],
"label": "ID non-target contaminants",
"name": "Kraken2",
"outputs": [
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}
},
"tool_id": "Cut1",
"tool_state": "{\"columnList\": \"c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"columnList\": \"c2\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.2",
"type": "tool",
"uuid": "8cc3e58f-2940-454a-9cf6-b32c1ab19016",
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},
"11": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
"errors": null,
"id": 11,
"input_connections": {
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"output_name": "out_file1"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool gfastats",
"name": "mode_condition"
},
{
"description": "runtime parameter for tool gfastats",
"name": "target_condition"
},
{
"description": "runtime parameter for tool gfastats",
"name": "target_condition"
}
],
"label": "removing scaffolds ",
"name": "gfastats",
"outputs": [
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"top": 798.078125
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1",
"tool_shed_repository": {
"changeset_revision": "3ef480892a9f",
"changeset_revision": "764f2516d837",
"name": "gfastats",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta.gz\", \"__current_case__\": 1, \"line_length\": null}, \"discover_paths\": false, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"true\", \"__current_case__\": 1, \"target_sequence\": \"\", \"include_bed\": {\"__class__\": \"ConnectedValue\"}, \"exclude_bed\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.3.6+galaxy0",
"tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"fasta.gz\", \"__current_case__\": 1, \"line_length\": null}, \"discover_paths\": false, \"sort\": \"\", \"remove_terminal_gaps\": false, \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"true\", \"__current_case__\": 1, \"target_sequence\": \"\", \"include_bed\": {\"__class__\": \"ConnectedValue\"}, \"exclude_bed\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.3.9+galaxy1",
"type": "tool",
"uuid": "5113c945-c811-4cbc-81ac-20d1d80e97ed",
"when": null,
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5 changes: 5 additions & 0 deletions workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/CHANGELOG.md
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# Changelog

## [0.4] 2024-12-16

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1`

## [0.3] 2024-08-26

- Changed the regex to only change the sequences. The workflow is now more robust to different (non VGP) scaffold names and VGP names with prefixes.
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