<tool id="imgt_locus_split" name="IMGT Locus Split" version="0.1">
    <requirements>
        <requirement type="package" version="0.4.13">python-magic</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python3 $__tool_directory__/imgt_locus_split.py 
            --input $input 
            --output-ig ${output_ig}
            --output-igh ${output_igh}
            --output-igk ${output_igk}
            --output-igl ${output_igl}
            --output-tr ${output_tr}
            --output-tra ${output_tra}
            --output-trb ${output_trb}
            --output-trd ${output_trd}
            --output-trg ${output_trg}
    ]]></command>
    <inputs>
        <param name="input" type="data" format="data" label="The IMGT zip file to be split"/>
        <param name="loci" type="select" label="Loci" multiple="true" display="checkboxes">
            <option value="IG" selected="true">IG</option>
            <option value="IGH">IGH</option>
            <option value="IGK">IGK</option>
            <option value="IGL">IGL</option>
            <option value="TR" selected="true">TR</option>
            <option value="TRA">TRA</option>
            <option value="TRB">TRB</option>
            <option value="TRD">TRD</option>
            <option value="TRG">TRG</option>
        </param>
    </inputs>
    <outputs>
        <data format="imgt_archive" name="output_ig" label="Filtered IMGT IG: ${input.name}">
            <filter>loci.__contains__('IG')</filter>
        </data>
        <data format="imgt_archive" name="output_igh" label="Filtered IMGT IGH: ${input.name}">
            <filter>loci.__contains__('IGH')</filter>
        </data>
        <data format="imgt_archive" name="output_igk" label="Filtered IMGT IGK: ${input.name}">
            <filter>loci.__contains__('IGK')</filter>
        </data>
        <data format="imgt_archive" name="output_igl" label="Filtered IMGT IGL: ${input.name}">
            <filter>loci.__contains__('IGL')</filter>
        </data>
        <data format="imgt_archive" name="output_tr" label="Filtered IMGT TR: ${input.name}">
            <filter>loci.__contains__('TR')</filter>
        </data>
        <data format="imgt_archive" name="output_tra" label="Filtered IMGT TRA: ${input.name}">
            <filter>loci.__contains__('TRA')</filter>
        </data>
        <data format="imgt_archive" name="output_trb" label="Filtered IMGT TRB: ${input.name}">
            <filter>loci.__contains__('TRB')</filter>
        </data>
        <data format="imgt_archive" name="output_trd" label="Filtered IMGT TRD: ${input.name}">
            <filter>loci.__contains__('TRD')</filter>
        </data>
        <data format="imgt_archive" name="output_trg" label="Filtered IMGT TRG: ${input.name}">
            <filter>loci.__contains__('TRG')</filter>
        </data>
    </outputs>
    <help><![CDATA[
        Creates a new IMGT zip file for every checked locus with sequences from only that locus.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/nar/gku1056</citation>
    </citations>
</tool>