view data_manager/ganon_data_manager.xml @ 3:c220590bde7a draft

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<tool id="ganon_data_manager" name="ganon data manager" version="0.0.1" tool_type="manage_data">
    <description>Fetch rRNA data from NCBI RefSeq and create ganon databases</description>
    <requirements>
        <requirement type="package">python</requirement>
        <requirement type="package">ganon</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
       python $__tool_directory__/fetch_ganon.py --rrna $rrna --output_directory $out_dir; 
       ganon build -d $rrna -i *.gz;
       mv $rrna.* $out_dir;
    ]]></command>
    <inputs>
        <param argument="rrna" type="select" label="Bacterial rRNA loci" multiple="true">
          <option value="5S">5S</option>
          <option value="16S">16S</option>
          <option value="23S">23S</option>
        </param>
        <param argument="out_dir" type="text" label="Output folder" value="/tool-data/ganon"/>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json"/>
    </outputs>
    <help><![CDATA[
    Retrieve RefSeq Bacterial rRNA Targeted Loci
    ]]>
    </help>
    <citations>
    </citations>
</tool>