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

<tool id="EMBOSS: pepcoil68" name="pepcoil" version="5.0.0">
  <description>Predicts coiled coil regions</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>pepcoil -sequence $input1 -outfile $out_file1 -window $window -coil $coil -frame $frame -other $other -auto</command>
  <inputs>
    <param format="data" name="input1" type="data">
      <label>Sequence</label>
    </param>
    <param name="window" size="4" type="text" value="28">
      <label>Window size</label>
    </param>
    <param name="coil" type="select">
      <label>Report coiled coil regions</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="frame" type="select">
      <label>Show coil frameshifts</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="other" type="select">
      <label>Report non coiled coil regions</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
  </inputs>
  <outputs>
    <data format="pepcoil" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="window" value="28"/>
      <param name="coil" value="yes"/>
      <param name="frame" value="yes"/>
      <param name="other" value="yes"/>
      <output name="out_file1" file="emboss_pepcoil_out.pepcoil"/>
    </test>
  </tests>
  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepcoil.html
  </help>
</tool>