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Merge pull request galaxyproject#383 from planemo-autoupdate/workflow…
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…s/data-fetching/sra-manifest-to-concatenated-fastqs

Updating workflows/data-fetching/sra-manifest-to-concatenated-fastqs from 0.3 to 0.4
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@lldelisle
lldelisle authored Apr 9, 2024
2 parents 396e912 + 4c10707 commit c334a0b
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6 changes: 6 additions & 0 deletions workflows/data-fetching/sra-manifest-to-concatenated-fastqs/CHANGELOG.md
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# Changelog

## [0.4] 2024-04-08

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1`
- `toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.10+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.0+galaxy0`

## [0.3] 2024-03-11

### Automatic update
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65 changes: 14 additions & 51 deletions .../data-fetching/sra-manifest-to-concatenated-fastqs/sra-manifest-to-concatenated-fastqs.ga
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}
],
"format-version": "0.1",
"release": "0.3",
"release": "0.4",
"license": "MIT",
"name": "sra_manifest_to_concatenated_fastqs_parallel",
"steps": {
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"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Cut",
"name": "columnList"
},
{
"description": "runtime parameter for tool Cut",
"name": "input"
}
],
"inputs": [],
"label": "Cut columns of interest",
"name": "Cut",
"outputs": [
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},
"6": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
"errors": null,
"id": 6,
"input_connections": {
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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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"top": 189
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "12615d397df7",
"changeset_revision": "fbf99087e067",
"name": "text_processing",
"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___$2\", \"is_regex\": true, \"global\": false, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "9.3+galaxy0",
"tool_version": "9.3+galaxy1",
"type": "tool",
"uuid": "7b4781ed-57b0-4962-a647-21e54375c195",
"when": null,
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"output_name": "out_file1"
}
},
"inputs": [
{
"description": "runtime parameter for tool Cut",
"name": "input"
}
],
"inputs": [],
"label": "Cut to get only SRA",
"name": "Cut",
"outputs": [
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},
"9": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.10+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.0+galaxy0",
"errors": null,
"id": 9,
"input_connections": {
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"output_name": "output_collection_other"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.10+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.0+galaxy0",
"tool_shed_repository": {
"changeset_revision": "de0f7e0a3896",
"changeset_revision": "ba931a59dd59",
"name": "sra_tools",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"adv\": {\"seq_defline\": \"@$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": "3.0.10+galaxy0",
"tool_version": "3.1.0+galaxy0",
"type": "tool",
"uuid": "fa409017-1eea-4426-83f6-22a10b9f762c",
"when": null,
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{
"description": "runtime parameter for tool Relabel identifiers",
"name": "how"
},
{
"description": "runtime parameter for tool Relabel identifiers",
"name": "input"
}
],
"label": "relabel pair collec to get SRA+sample",
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{
"description": "runtime parameter for tool Relabel identifiers",
"name": "how"
},
{
"description": "runtime parameter for tool Relabel identifiers",
"name": "input"
}
],
"label": "relabel single collec to get SRA+sample",
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"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Apply rules",
"name": "input"
}
],
"inputs": [],
"label": null,
"name": "Apply rules",
"outputs": [
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"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Apply rules",
"name": "input"
}
],
"inputs": [],
"label": null,
"name": "Apply rules",
"outputs": [
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