<tooll id="extract_contigs" name="Extract contigs from RepeatExplorer2 archive" version="1.0.0.3">
  <command detect_errors="exit_code">
     <![CDATA[
    unzip -p ${RepeatExplorer_archive} contigs.fasta  > ${contigs}
    &&
    mkdir -p tempdir
    &&
    unzip ${RepeatExplorer_archive} "*.aln" -d tempdir
    &&
    find tempdir -type f -name "*.aln" -exec cat {} + > ${aln}
    &&
    rm -r tempdir
    ]]>
  </command>


  <inputs>
    <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results" type="data" format="zip"/>
  </inputs>

  <outputs>
    <data name="contigs" format="fasta" label="Contigs from RepeatExplorer clustering from data ${RepeatExplorer_archive.hid}" />
    <data name="aln" format="txt" label="Contigs from RepeatExplorer clustering in aln format from data ${RepeatExplorer_archive.hid}" />
  </outputs>
</tooll>