Mercurial > repos > estrain > data_manager_mlst
diff data_manager/data_manager_mlst.xml @ 0:a9ff6184213f draft default tip
planemo upload commit bdb45cf3a98e21f5002866b6789a1457f521bf5d
| author | estrain |
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| date | Thu, 12 Mar 2026 20:06:31 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_mlst.xml Thu Mar 12 20:06:31 2026 +0000 @@ -0,0 +1,47 @@ +<tool id="data_manager_mlst" + name="MLST Data Manager" + tool_type="manage_data" + version="1.0.1" + profile="22.05"> + + <description>Download and build PubMLST BLAST databases</description> + + <requirements> + <requirement type="package" version="2.23.0">mlst</requirement> + <requirement type="package" version="2.14.1">blast</requirement> + </requirements> + + <command detect_errors="exit_code"><![CDATA[ +python '$__tool_directory__/data_manager_mlst.py' '$output_file' + ]]></command> + + <inputs> + <param name="source" type="hidden" value="pubmlst"/> + </inputs> + + <outputs> + <data name="output_file" format="data_manager_json"/> + </outputs> + + <help><![CDATA[ +This Data Manager downloads all **PubMLST** databases using the +`mlst-download_pub_mlst` command (from Torsten Seemann’s *MLST* 2.23.0), +then merges and indexes them into a single **BLAST+** nucleotide database +for use by Galaxy MLST tools. + +A data table entry will be added under **mlst** containing the timestamped +database name and path. + ]]></help> + + <citations> + <citation type="bibtex"> +@misc{seemann_mlst, + author={Torsten Seemann}, + title={mlst: Scan contig files against PubMLST typing schemes}, + year={2025}, + howpublished={https://github.com/tseemann/mlst} +} + </citation> + </citations> +</tool> +
