view glang-galaxy-conf/gembassy/gcodoncompiler.xml @ 2:8947fca5f715 draft default tip

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<tool id="EMBOSS: gcodoncompiler" name="gcodoncompiler" version="1.0.2">
  <description>Calculates various kinds of amino acid and codon usage data</description>
  <command>gcodoncompiler -sequence $input1 -translate $translate -startcodon $startcodon -stopcodon $stopcodon -data $data -auto -noaccid -outfile $out_file1</command>
  <inputs>
  <param format="data" name="input1" type="data">
    <label>Sequence</label>
  </param>
    <param name="translate" type="select" value="no">
      <label>Include to translate using standard codon table</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="startcodon" type="select" value="no">
      <label>Include to include start codon</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="stopcodon" type="select" value="no">
      <label>Include to include stop codon</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="data" type="select" value="R0">
      <label>Kinds of codon usage data. R* hypothesizes amino acids which are not present in the gene</label>
      <option value="A0">Absolute amino acid frequency ('AA')</option>
      <option value="A1">Relative amino acid frequency ('RAAU')</option>
      <option value="C0">Absolute codon frequency ('AF')</option>
      <option value="C1">Relative codon frequency in a complete sequence</option>
      <option value="C2">Relative codon frequency in each amino acid ('RF')</option>
      <option value="C3">Relative synonymous codon usage ('RSCU')</option>
      <option value="C4">Relative adaptiveness; i.e., ratio to maximum of minor codon (W)</option>
      <option value="C5">Maximum (1) or minor (0) codonAbsolute codon frequency ('AF')</option>
      <option value="R0">Absolute codon frequency</option>
      <option value="R1">Relative codon frequency in a complete sequence</option>
      <option value="R2">Relative codon frequency in each amino acid ('RF')</option>
      <option value="R3">Relative synonymous codon usage ('RSCU')</option>
      <option value="R4">Relative adaptiveness; i.e., ratio to maximum of minor codon (W)</option>
      <option value="R5">Maximum (1) or minor (0) codon</option>
    </param>
  </inputs>
  <outputs>
    <data format="csv" name="out_file1" label="${tool.name} for ${input1.name}" />    
  </outputs>
</tool>