<tool id="hint" name="Hint" version="HINT: 1.1.1">
    <description> predicts TFBSs given open chromatin data </description>
    <requirements>
      <requirement type="package">pymodules</requirement>
    </requirements>
    <command interpreter="python">
      hint_wrapper.py
      --input $input
      --region $region
      --out-dir $output.extra_files_path
      --output $output
    </command>
      <inputs>
         <param format="bam" help="" name="input" optional="false" type="data" label="Input BAM"/>
         <param format="bed" help="" name="region" optional="false" type="data" label="Input BED"/>
      </inputs>
      <outputs>
         <data format="bed" label="${tool.name} on ${on_string}" name="output"/>
      </outputs>
      <help>
      </help>
</tool>