<tool id="EMBOSS: matcher52" name="matcher" version="5.0.0">
  <description>Finds the best local alignments between two sequences</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>matcher -asequence $input1 -bsequence $input2 -outfile $out_file1 -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -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="alternatives" size="4" type="text" value="1">
      <label>Number of alternative matches</label>
    </param>
    <param name="gapopen" size="4" type="text" value="16">
      <label>Gap penalty</label>
    </param>
    <param name="gapextend" size="4" type="text" value="4">
      <label>Gap length (extension) penalty</label>
    </param>
    <param name="out_format1" type="select">
      <label>Output Alignment File Format</label>
      <option value="markx0">Markx0 (p)</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="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>
  </inputs>
  <outputs>
    <data format="markx0" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="input2" value="1.fasta"/>
      <param name="alternatives" value="1"/>
      <param name="gapopen" value="16"/>
      <param name="gapextend" value="4"/>
      <param name="out_format1" value="fasta"/>
      <output name="out_file1" file="emboss_matcher_out.fasta"/>
    </test>
  </tests>
  <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/matcher.html
  </help>
</tool>