Mercurial > repos > recetox > data_manager_recetox_metabolite_fetcher

view data_manager/recetox_metabolite_fetcher.xml @ 0:953dd78a34d3 draft default tip

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"planemo upload commit be4b24b2dacc3f23538068d5a6082bca246f6887"
author recetox
date Tue, 25 Aug 2020 11:15:49 +0000
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<tool id="recetox_metabolite_fetcher" name="Metabolite Fetcher" version="1.0.0" tool_type="manage_data">
    <requirements>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
        python '${__tool_directory__}/recetox_metabolite_fetcher.py'
            --tool_data_dir '${__tool_directory__}'
            --database_url '${url}'
            --data_manager_json '${out_file}'
    ]]></command>
    
    <inputs>
        <param name="url" type="text" label="Database url" help="Type custom url or select url from a predefined list a metabolite databases.">
            <option value="https://hmdb.ca/system/downloads/3.6/hmdb_metabolites.zip">HMDB 3.6</option>
            <option value="https://hmdb.ca/system/downloads/current/hmdb_metabolites.zip">HMDB 4.0</option>
            <option value="http://www.t3db.ca/system/downloads/current/toxins.xml.zip">T3DB</option>
        </param>
    </inputs>
    
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    
    <help><![CDATA[
        Downloads a snapshot of a specified metabolite database and stores it withing the whole Galaxy instance.
    ]]></help>
    
    <citations>
        <citation type="doi">https://doi.org/10.1093/nar/gkl923</citation>
        <citation type="doi">https://doi.org/10.1093/nar/gkn810</citation>
        <citation type="doi">https://doi.org/10.1093/nar/gks1065</citation>
        <citation type="doi">https://doi.org/10.1093/nar/gkx1089</citation>
    </citations>
</tool>