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

<tool id="EMBOSS: pepnet70" name="pepnet" version="5.0.0">
  <!-- graphical output file with path information -->
  <description>Displays proteins as a helical net</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>pepnet -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic $amphipathic -auto</command>
  <inputs>
    <param format="data" name="input1" type="data">
      <label>Sequence</label>
    </param>
    <param name="squares" size="10" type="text" value="ILVM">
      <label>Residues to mark with squares</label>
    </param>
    <param name="diamonds" size="10" type="text" value="DENQST">
      <label>Residues to mark with diamonds</label>
    </param>
    <param name="octags" size="10" type="text" value="HKR ">
      <label>Residues to mark with octagons</label>
    </param>
    <param name="amphipathic" type="select">
      <label>If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified</label>
      <option value="no">No</option>
      <option value="yes">Yes</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/pepnet.html
  </help>
</tool>