<tool id="EMBOSS: maskfeat50" name="maskfeat" version="5.0.0">

  <description>Mask off features of a sequence</description>

  <command>maskfeat -sequence $input1 -outseq $out_file1 -type "$type" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto</command>

  <inputs>

    <param format="data" name="input1" type="data">

      <label>Sequence</label>

    </param>

    <param name="type" size="50" type="text" value="repeat*">

      <label>Feature to mask</label>

    </param>

    <param name="tolower" type="select">

      <label>Mask features by converting to lowercase</label>

      <option value="no">No</option>

      <option value="yes">Yes</option>

    </param>

    <param name="maskchar" size="1" type="text" value="N">

      <label>Character to mask with</label>

    </param>

    <param name="out_format1" type="select">

      <label>Output Sequence File Format</label>

      <option value="fasta">FASTA (m)</option>

      <option value="acedb">ACeDB (m)</option>

      <option value="asn1">ASN.1 (m)</option>

      <option value="clustal">Clustal (m)</option>

      <option value="codata">CODATA (m)</option>

      <option value="embl">EMBL (m)</option>

      <option value="fitch">Fitch (m)</option>

      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>

      <option value="genbank">GENBANK (m)</option>

      <option value="gff">GFF (m)</option>

      <option value="hennig86">Hennig86 (m)</option>

      <option value="ig">Intelligenetics (m)</option>

      <option value="jackknifer">Jackknifer (m)</option>

      <option value="jackknifernon">Jackknifernon (m)</option>

      <option value="mega">Mega (m)</option>

      <option value="meganon">Meganon (m)</option>

      <option value="msf">Wisconsin Package GCG's MSF (m)</option>

      <option value="pir">NBRF (PIR) (m)</option>

      <option value="ncbi">NCBI style FASTA (m)</option>

      <option value="nexus">Nexus/PAUP (m)</option>

      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>

      <option value="phylip">PHYLIP interleaved (m)</option>

      <option value="phylipnon">PHYLIP non-interleaved (m)</option>

      <option value="selex">SELEX (m)</option>

      <option value="staden">Staden (s)</option>

      <option value="strider">DNA strider (m)</option>

      <option value="swiss">SwisProt entry (m)</option>

      <option value="text">Plain sequence (s)</option>

      <option value="treecon">Treecon (m)</option>

    </param>

  </inputs>

  <outputs>

    <data format="fasta" name="out_file1" />

  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="type" value="repeat*"/>
      <param name="tolower" value="no"/>
      <param name="maskchar" value="N"/>
      <param name="out_format1" value="fasta"/>
      <output name="out_file1" file="emboss_maskfeat_out.fasta"/>
    </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/maskfeat.html
  </help>
</tool>