<tool id="removeExonLines" name="remove exon lines">
  <description>Removes the introns of the transcript files.</description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
  <command interpreter="python"> ../Java/Python/RemoveExons.py -i $inputFile -f gff3 -o $outputFile  </command>
  <inputs>
		<param name="inputFile" format="gff3" type="data" label="Input File"/>
  </inputs>

  <outputs>
    <data format="gff3" name="outputFile" label="[remove introns] output file"/>
  </outputs>

  <help>
	Simply remove the introns of the input file, thus getting the unmatured transcript.
  </help>
</tool>