root/galaxy-central/tools/emboss_5/emboss_dreg.xml @ 3

<tool id="EMBOSS: dreg27" name="dreg" version="5.0.0">
  <description>Regular expression search of a nucleotide sequence</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>dreg -sequence $input1 -outfile $out_file1 -pattern "$pattern" -raccshow3 "no" -rusashow3 "no" -rdesshow3 "no" -auto</command>
  <inputs>
    <param format="data" name="input1" type="data">
      <label>Sequence 1</label>
    </param>
    <param name="pattern" size="50" type="text" value="(AUG)">
      <label>Regular expression pattern</label>
    </param>
  </inputs>
  <outputs>
    <data format="dreg" name="out_file1" />
  </outputs>
  <!-- tests not possible since dreg timestamps output file -->  
  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dreg.html
  </help>
</tool>