<tool id="EMBOSS: coderet13" name="coderet" version="5.0.0">
  <description>Extract CDS, mRNA and translations from feature tables</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <!--  <command>coderet -seqall $input1 -outfile $out_file1 -osformat2 $out_format1 -cds $cds -mrna $mrna -translation $translation -auto</command>-->
  <command>coderet -seqall $input1 -outfile $out_file1 -auto</command>
  <inputs>
    <param format="data" name="input1" type="data">
      <label>On query</label>
    </param>
    <!--
    <param name="cds" type="boolean" truevalue="yes" falsevalue="no" checked="true">
      <label>Extract CDS sequences</label>
    </param>
    <param name="mrna" type="select">
      <label>Extract mRNA sequences</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="translation" type="select">
      <label>Extract translated sequences</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </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="coderet" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <output name="out_file1" file="emboss_coderet_out.coderet"/>
    </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/coderet.html
  </help>
</tool>