<tool id="extract_re_contigs" name="Extract Repeat Library from RepeatExplorer Archive" version="0.1.1" python_template_version="3.5">
    <requirements>
        <requirement type="package" version="3">python</requirement>
    </requirements>
    <required_files>
        <include type="literal" path="get_contigs_from_re_archive.py"/>
    </required_files>
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/get_contigs_from_re_archive.py -re '$re_archive' -m '$min_coverage' -L '$min_length' -f '$contigs'
    ]]></command>
    <inputs>
        <param type="data" name="re_archive" format="zip" label="RepeatExplorer archive"/>
        <param type="integer" name="min_coverage" value="5" min="1" max="100" label="minimal read depth coverage of contigs" help="region with lower coverage are trimmed off or hardmasked"/>
        <param type="integer" name="min_length" value="50" min="10" lebel="Minimum length of extracted contigs" />
    </inputs>
    <outputs>
        <data name="contigs" format="fasta" label="Contigs(Repeat library) extracted from RepeatExplorer archive ${re_archive.hid}"/>
    </outputs>
    <help><![CDATA[
        This tool extracts contigs and TAREAN concesus from RepeatExplorer archive in fasta format. Sequences with reads depth smaller that threshold are removed. Contigs shorter that specied threshold ere also filtered  out. Filtering does not affect TAREAN consensus. Extracted sequences have Id in format CLXContigY where X is cluster ID and Y is number of contig. 
    ]]></help>
</tool>