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<tool id="trams" name="TRAMS">
  <description>Tool for Rapid Annotation of Microbial SNPs</description>
  <command interpreter="python">trams.py $input1 $input2 $ref_format $annot $overl $sum</command>
  <inputs>
    <param name="input1" type="data" format="tabular" label="SNP table" />
    <param name="input2" type="data" format="txt" label="Reference genome" help="Reference genome file, should be genbank or embl file." />
    <param name="ref_format" type="select">
     <label>Reference file type</label>
      <option value="gb">Genbank</option>
      <option value="embl">EMBL</option>
    </param>
  </inputs>
  <outputs>
    <data name="annot" format="tabular" label="${tool.name} on ${on_string}: SNP annotation file" />
    <data name="overl" format="tabular" label="${tool.name} on ${on_string}: Overlap file" />
    <data name="sum" format="txt" label="${tool.name} on ${on_string}: Summary file" />
  </outputs>
  <help>

This tool annotates SNPs from a SNP table and a genbank file.

  </help>
</tool>