<tool id="phytab_clearcut" name="phytab clearcut">
  <description>clearcut: Generate Neighbor Joining phylogeny. Input can be fasta or phytab format.</description>
  <requirements>
    <requirement type="package">clearcut</requirement>
  </requirements>
  <command interpreter="python">
    phytab_clearcut.py -i $data -t $datatype > $clearcut_stdout 2>&amp;1
  </command>
  <inputs>
    <param format="txt" name="data" type="data" label="Sequence data" help="This should be sequence data in phytab or fasta"/>
    <param name="datatype" type="select" format="text">
      <label>Type of data for all partitions</label>
      <option value="P">Protein</option> 
	<option value="D">DNA</option> 
    </param>
  </inputs>
  <outputs>
    <data format="txt" name="clearcut_stdout" label="${tool.name} on ${on_string}: stdout" />
    <data format="tabular" name="clearcut_results" label="${tool.name} on ${on_string}: results" from_work_dir="data/results.data" />
  </outputs>
  <tests>
  </tests>
  <help>
  </help>
</tool>