<tool id="EMBOSS: digest23" name="digest" version="5.0.0">
  <description>Protein proteolytic enzyme or reagent cleavage digest</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>digest -seqall '$input1' -outfile '$out_file1' -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequence" />
    <param name="menu" type="select" label="Enzyme/Reagent">
      <option value="1">Trypsin</option>
      <option value="2">Lys-C</option>
      <option value="3">Arg-C</option>
      <option value="4">Asp-N</option>
      <option value="5">V8-bicarb</option>
      <option value="6">V8-phosph</option>
      <option value="7">Chymotrypsin</option>
      <option value="8">CNBr</option>
    </param>
    <param name="unfavoured" type="select" label="Trypsin will not normally cut after a K if it is followed by (e.g.) another K or a P. Specifying this shows those cuts, as well as the favoured ones">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="overlap" type="select" label="Used for partial digestion. Shows all cuts from favoured cut sites plus 1..3, 2..4, 3..5 etc but not (e.g.) 2..5. Overlaps are therefore fragments with exactly one potential cut site within it">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="allpartials" type="select" label="As for overlap but fragments containing more than one potential cut site are included">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="out_format1" type="select" label="Output report file format">
      <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="srs">SRS</option>
      <option value="table">Table</option>
      <option value="tagseq">TagSeq</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="digest" />
  </outputs>
  <help>
    You can view the original documentation here_.

    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/digest.html
  </help>
  <expand macro="citations" />
</tool>