root/galaxy-central/tools/emboss_5/emboss_diffseq.xml

<tool id="EMBOSS: diffseq22" name="diffseq" version="5.0.0">
  <description>Find differences between nearly identical sequences</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <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 format="data" name="input1" type="data">
      <label>Sequence 1</label>
    </param>
    <param format="data" name="input2" type="data">
      <label>Sequence 2</label>
    </param>
    <param name="wordsize" size="4" type="text" value="20">
      <label>Wordsize</label>
    </param>
    <param name="globaldifferences" type="select">
      <label>Report differences at the ends</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="out_format1" type="select">
      <label>Output Report File Format</label>
      <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</label>
      <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</label>
      <option value="gff">GFF</option>
      <option value="embl">EMBL</option>
      <option value="swiss">SwissProt</option>
    </param>
  </inputs>
  <outputs>
    <data format="diffseq" name="out_file1" />
    <data format="gff" name="out_file2" />
    <data format="gff" name="out_file3" />
  </outputs>
  <code file="emboss_format_corrector.py" />
  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/diffseq.html
  </help>
</tool>