annotate extract_contigs_from_archive.xml @ 20:5a05925340b0 draft

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<tool id="extract_contigs" name="Extract contigs from RepeatExplorer2 archive">
  <command detect_errors="exit_code">
    unzip -p ${RepeatExplorer_archive} contigs.fasta  &gt; ${contigs}
    &amp;&amp;
    unzip -p -j ${RepeatExplorer_archive} "*.aln"  &gt; ${aln}
  </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>
</tool>