<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



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**Citation**



If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
  </help>
</tool>