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