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

<tool id="EMBOSS: pepinfo69" name="pepinfo" version="5.0.0">
  <!-- puts file info in output files -->
  <description>Plots simple amino acid properties in parallel</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepinfo -sequence $input1 -outfile $out_file1 -goutfile $out_file2 -graph png -hwindow $hwindow $plot_type -auto</command>
  <inputs>
    <param format="data" name="input1" type="data">
      <label>Sequence</label>
    </param>
    <param name="hwindow" size="4" type="text" value="9">
      <label>Window size for hydropathy averaging</label>
    </param>
    <param name="plot_type" type="select">
      <label>Choose a plot type</label>
      <option value="-generalplot yes -hydropathyplot no">Histogram of general properties</option>
      <option value="-generalplot no -hydropathyplot yes">Graphs of hydropathy</option>
    </param>
  </inputs>
  <outputs>
    <data format="pepinfo" name="out_file1" />
    <data format="png" name="out_file2" />
  </outputs>
  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepinfo.html
  </help>
</tool>