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

<tool id="EMBOSS: octanol63" name="octanol" version="5.0.0">
  <!-- graphics output with filename, no functional tests added -->  
  <description>Displays protein hydropathy</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command interpreter="perl">emboss_single_outputfile_wrapper.pl octanol -sequence $input1 -graph png -goutfile $out_file1 -width $width -octanolplot $octanolplot -interfaceplot $interfaceplot
  -differenceplot $differenceplot -auto</command>
  <inputs>
    <param format="data" name="input1" type="data">
      <label>Sequences</label>
    </param>
    <param name="width" size="4" type="text" value="19">
      <label>Window size</label>
    </param>
    <param name="octanolplot" type="select">
      <label>Display the octanol plot</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="interfaceplot" type="select">
      <label>Display the interface plot</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="differenceplot" type="select">
      <label>Display the difference plot</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
  </inputs>
  <outputs>
    <data format="png" name="out_file1" />
  </outputs>
  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/octanol.html
  </help>
</tool>