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

<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.1">
  <description>Nucleic acid pattern search</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>Sequences</label>
    </param>
    <param name="pattern" size="5" type="text" value="">
      <label>Search pattern</label>
      <sanitizer>
        <valid initial="string.printable">
         <remove value="&apos;"/>
        </valid>
        <mapping initial="none">
          <add source="&apos;" target=""/>
        </mapping>
      </sanitizer>
    </param>
    <param name="mismatch" size="5" type="text" value="0">
      <label>Number of mismatches</label>
    </param>
    <param name="complement" type="select">
      <label>Search complementary strand</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="out_format1" type="select">
      <label>Output Report File Format</label>
      <option value="seqtable">SeqTable</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="dbmotif">DbMotif</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="simple">SRS Simple</option>
      <option value="fuzznuc">Fuzznuc Output File</option>
      <option value="srs">SRS</option>
      <option value="table">Table</option>
      <option value="tagseq">TagSeq</option>
    </param>
  </inputs>
  <outputs>
    <data format="fuzznuc" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="pattern" value="AA"/>
      <param name="mismatch" value="0"/>
      <param name="complement" value="no"/>
      <param name="out_format1" value="excel"/>
      <output name="out_file1" file="emboss_fuzznuc_out.tabular"/>
    </test>
  </tests>
  <code file="emboss_format_corrector.py" />
  <help>

.. class:: warningmark

The input dataset needs to be sequences.

-----

    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzznuc.html
  </help>
</tool>