Mercurial > repos > estrain > data_manager_mlst
comparison data_manager/data_manager_mlst.xml @ 0:a9ff6184213f draft default tip
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| author | estrain |
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| date | Thu, 12 Mar 2026 20:06:31 +0000 |
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| -1:000000000000 | 0:a9ff6184213f |
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| 1 <tool id="data_manager_mlst" | |
| 2 name="MLST Data Manager" | |
| 3 tool_type="manage_data" | |
| 4 version="1.0.1" | |
| 5 profile="22.05"> | |
| 6 | |
| 7 <description>Download and build PubMLST BLAST databases</description> | |
| 8 | |
| 9 <requirements> | |
| 10 <requirement type="package" version="2.23.0">mlst</requirement> | |
| 11 <requirement type="package" version="2.14.1">blast</requirement> | |
| 12 </requirements> | |
| 13 | |
| 14 <command detect_errors="exit_code"><![CDATA[ | |
| 15 python '$__tool_directory__/data_manager_mlst.py' '$output_file' | |
| 16 ]]></command> | |
| 17 | |
| 18 <inputs> | |
| 19 <param name="source" type="hidden" value="pubmlst"/> | |
| 20 </inputs> | |
| 21 | |
| 22 <outputs> | |
| 23 <data name="output_file" format="data_manager_json"/> | |
| 24 </outputs> | |
| 25 | |
| 26 <help><![CDATA[ | |
| 27 This Data Manager downloads all **PubMLST** databases using the | |
| 28 `mlst-download_pub_mlst` command (from Torsten Seemann’s *MLST* 2.23.0), | |
| 29 then merges and indexes them into a single **BLAST+** nucleotide database | |
| 30 for use by Galaxy MLST tools. | |
| 31 | |
| 32 A data table entry will be added under **mlst** containing the timestamped | |
| 33 database name and path. | |
| 34 ]]></help> | |
| 35 | |
| 36 <citations> | |
| 37 <citation type="bibtex"> | |
| 38 @misc{seemann_mlst, | |
| 39 author={Torsten Seemann}, | |
| 40 title={mlst: Scan contig files against PubMLST typing schemes}, | |
| 41 year={2025}, | |
| 42 howpublished={https://github.com/tseemann/mlst} | |
| 43 } | |
| 44 </citation> | |
| 45 </citations> | |
| 46 </tool> | |
| 47 |