<tool id="EMBOSS: diffseq22" name="diffseq" version="5.0.0.1">
  <description>Find differences between nearly identical sequences</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>diffseq -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize $wordsize -globaldifferences $globaldifferences -rformat3
  $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequence 1" />
    <param name="input2" type="data" format="data" label="Sequence 2" />
    <param name="wordsize" type="integer" value="20" label="Wordsize" />
    <param name="globaldifferences" type="select" label="Report differences at the ends">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="out_format1" type="select" label="Output report file format">
      <option value="diffseq">Diffseq</option>
      <option value="embl">EMBL</option>
      <option value="genbank">GENBANK</option>
      <option value="gff">GFF</option>
      <option value="pir">PIR</option>
      <option value="swiss">SwissProt</option>
      <option value="dbmotif">DbMotif</option>
      <option value="excel">Excel (tab delimited)</option>
      <option value="feattable">FeatTable</option>
      <option value="motif">Motif</option>
      <option value="regions">Regions</option>
      <option value="seqtable">SeqTable</option>
      <option value="simple">SRS Simple</option>
      <option value="srs">SRS</option>
      <option value="table">Table</option>
      <option value="tagseq">TagSeq</option>
    </param>
    <param name="out_format2" type="select" label="Sequence 1 output feature file format">
      <option value="gff">GFF</option>
      <option value="embl">EMBL</option>
      <option value="swiss">SwissProt</option>
    </param>
    <param name="out_format3" type="select" label="Sequence 2 output feature file format">
      <option value="gff">GFF</option>
      <option value="embl">EMBL</option>
      <option value="swiss">SwissProt</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="diffseq" />
    <data name="out_file2" format="gff" />
    <data name="out_file3" format="gff" />
  </outputs>
  <help>
    You can view the original documentation here_.

    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/diffseq.html
  </help>
  <expand macro="citations" />
</tool>