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Updating workflows/data-fetching/sra-manifest-to-concatenated-fastqs …
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…from 0.1 to 0.2
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planemo-autoupdate committed Nov 10, 2023
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# Changelog

## [0.2] 2023-11-10

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.5+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy0`
- `toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1` was updated to `toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.2`

## [0.1] 2023-10-23
First release.
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}
],
"format-version": "0.1",
"release": "0.1",
"release": "0.2",
"license": "MIT",
"name": "sra_manifest_to_concatenated_fastqs_parallel",
"steps": {
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"output_name": "out_file1"
}
},
"inputs": [
{
"description": "runtime parameter for tool Replace",
"name": "infile"
}
],
"inputs": [],
"label": "generate table for relabelling",
"name": "Replace",
"outputs": [
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"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"[^\\\\w\\\\- .,\\\\t](?=[^\\\\t]+$)\", \"replace_pattern\": \"-\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}, {\"__index__\": 1, \"find_pattern\": \"(.+)\\\\t(.+)\", \"replace_pattern\": \"$1\\\\t$1___$2\", \"is_regex\": true, \"global\": false, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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"tool_version": "1.1.4",
"type": "tool",
"uuid": "7b4781ed-57b0-4962-a647-21e54375c195",
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},
"9": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.5+galaxy3",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy0",
"errors": null,
"id": 9,
"input_connections": {
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"output_name": "output_collection_other"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.5+galaxy3",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy0",
"tool_shed_repository": {
"changeset_revision": "734abc7ac21d",
"changeset_revision": "6591f049cf7e",
"name": "sra_tools",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adv\": {\"seq_defline\": \"@$sn/$ri\", \"minlen\": null, \"split\": \"--split-3\", \"skip_technical\": true}, \"input\": {\"input_select\": \"file_list\", \"__current_case__\": 2, \"file_list\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.0.5+galaxy3",
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"type": "tool",
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"when": null,
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},
"14": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1",
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"errors": null,
"id": 14,
"input_connections": {
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"output_name": "paired_output"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.2",
"tool_shed_repository": {
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"changeset_revision": "5b2cc63d7a21",
"name": "concatenate_multiple_datasets",
"owner": "artbio",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dataset_names\": false, \"global_condition\": {\"input_type\": \"paired_collection\", \"__current_case__\": 1, \"inputs\": {\"__class__\": \"ConnectedValue\"}, \"paired_cat_type\": \"by_strand\"}, \"headers\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.4.1",
"tool_version": "1.4.2",
"type": "tool",
"uuid": "37b6fecb-1c87-4c41-8598-95d43b418ee0",
"when": null,
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},
"15": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1",
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"errors": null,
"id": 15,
"input_connections": {
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"output_name": "out_file1"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.2",
"tool_shed_repository": {
"changeset_revision": "55cf9d9defd1",
"changeset_revision": "5b2cc63d7a21",
"name": "concatenate_multiple_datasets",
"owner": "artbio",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__input_ext\": \"fastqsanger.gz\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"dataset_names\": false, \"global_condition\": {\"input_type\": \"singles\", \"__current_case__\": 0, \"inputs\": {\"__class__\": \"ConnectedValue\"}}, \"headers\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.4.1",
"tool_version": "1.4.2",
"type": "tool",
"uuid": "49a70885-3374-4680-bbd2-ad57b8be543d",
"when": null,
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