Mercurial > repos > estrain > data_manager_mlst

<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>
author	estrain
date	Thu, 12 Mar 2026 20:06:31 +0000
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