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

<tool id="EMBOSS: water107" name="water" version="5.0.0">
  <description>Smith-Waterman local alignment</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>water -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen "$gapopen" -gapextend "$gapextend" -brief $brief -aformat3 $out_format1 -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="gapopen" size="6" type="text" value="10.0">
      <label>Gap open penalty</label>
    </param>
    <param name="gapextend" size="6" type="text" value="0.5">
      <label>Gap extension penalty</label>
    </param>
    <param name="brief" type="select">
      <label>Brief identity and similarity</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="out_format1" type="select">
      <label>Output Alignment File Format</label>
      <option value="srs">SRS (m)</option>
      <option value="simple">Simple (m)</option>
      <option value="fasta">FASTA (m)</option>
      <option value="msf">MSF (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>
  </inputs>
  <outputs>
    <data format="srs" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="input2" value="1.fasta"/>
      <param name="gapopen" value="10.0"/>
      <param name="gapextend" value="0.5"/>
      <param name="brief" value="no"/>
      <param name="out_format1" value="score"/>
      <output name="out_file1" file="emboss_water_out.score"/>
    </test>
  </tests>
  <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/water.html
  </help>
</tool>