<tool id="EMBOSS: wordmatch110" name="wordmatch" version="5.0.0">
  <description>Finds all exact matches of a given size between 2 sequences</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2
  -offormat5 $out_format3 -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>Sequence 1</label>
    </param>
    <param format="fasta" name="input2" type="data">
      <label>Sequence 2</label>
    </param>
    <param name="wordsize" size="5" type="text" value="4">
      <label>Word size</label>
    </param>
    <param name="out_format1" type="select">
      <label>Output Alignment File Format</label>
      <option value="match">Match (m)</option>
      <option value="simple">Simple (m)</option>
      <option value="fasta">FASTA (m)</option>
      <option value="msf">MSF (m)</option>
      <option value="srs">SRS (m)</option>
      <option value="pair">Pair (p)</option>
      <option value="markx0">Markx0 (p)</option>
      <option value="markx1">Markx1 (p)</option>
      <option value="markx2">Markx2 (p)</option>
      <option value="markx3">Markx3 (p)</option>
      <option value="markx10">Markx10 (p)</option>
      <option value="srspair">SRS pair (p)</option>
      <option value="score">Score (p)</option>
    </param>
    <param name="out_format2" type="select">
      <label>Output Feature 1 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>Output Feature 2 File Format</label>
      <option value="gff">GFF</option>
      <option value="embl">EMBL</option>
      <option value="swiss">SwissProt</option>
    </param>
  </inputs>
  <outputs>
    <data format="match" name="out_file1" />
    <data format="gff" name="out_file2" />
    <data format="gff" name="out_file3" />
  </outputs>
  <!--   <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="input2" value="1.fasta"/>
      <param name="wordsize" value="4"/>
      <param name="out_format1" value="fasta"/>
      <param name="out_format2" value="gff"/>
      <param name="out_format3" value="gff"/>
      <output name="ofile2" file="emboss_wordmatch_out.embl"/>
    </test> 
  </tests> test takes a long time to run-->
  <code file="emboss_format_corrector.py" />
  <help>

.. class:: warningmark 

The input datasets need to be sequences. 

----- 

    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.html
  </help>
</tool>