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

<tool id="EMBOSS: patmatdb67" name="patmatdb" version="5.0.0">
  <description>Search a protein sequence with a motif</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>patmatdb -sequence $input1 -outfile $out_file1 -motif "$motif" -rformat3 $out_format1 -auto</command>
  <inputs>
    <param format="data" name="input1" type="data">
      <label>Main sequence</label>
    </param>
    <param name="motif" size="4" type="text" value="">
      <label>Motif to search for</label>
    </param>
    <param name="out_format1" type="select">
      <label>Output Report File Format</label>
      <option value="dbmotif">DbMotif</option>
      <option value="embl">EMBL</option>
      <option value="genbank">GENBANK</option>
      <option value="gff">GFF</option>
      <option value="pir">PIR</option>
      <option value="swiss">SwissProt</option>
      <option value="diffseq">Diffseq</option>
      <option value="excel">Excel (tab delimited)</option>
      <option value="feattable">FeatTable</option>
      <option value="motif">Motif</option>
      <option value="regions">Regions</option>
      <option value="seqtable">SeqTable</option>
      <option value="simple">SRS Simple</option>
      <option value="srs">SRS</option>
      <option value="table">Table</option>
      <option value="tagseq">TagSeq</option>
    </param>
  </inputs>
  <outputs>
    <data format="dbmotif" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="motif" value="aa"/>
      <param name="out_format1" value="excel"/>
      <output name="out_file1" file="emboss_patmatdb_out.tabular"/>
    </test>
  </tests>
  <code file="emboss_format_corrector.py" />
  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/patmatdb.html
  </help>
</tool>