<tool id="fimo_to_bed" name="FIMO-to-BED">
  <description>convert FIMO output to BED</description>
  <command interpreter="python">fimo_to_bed.py $input $rc > $output</command>
  <inputs>
    <param name="input" format="txt" type="data" label="FIMO output file"/>
    <param name="rc" label="Check if the sequences are reverse complement" type="boolean" truevalue="rc" falsevalue="none" checked="False"/>
  </inputs>
  <outputs>
    <data format="bed" name="output" />
  </outputs>
  <help>

  Only works if your original FIMO input fasta sequences have ids like:: 
  
    mm9_chr15_99358448_99360448_-
  
  
  </help>
</tool>