<tool id="removeIntrons" name="remove introns">
  <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 $formatType.inputFileName -f $formatType.FormatInputFileName -o $outputFile  </command>
  <inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName" type="select" label="query File Format">
				<option value="bed">bed</option>
				<option value="gff">gff</option>
				<option value="gff2">gff2</option>
				<option value="gff3">gff3</option>
				<option value="sam">sam</option>
				<option value="gtf">gtf</option>
			</param>
			<when value="bed">
				<param name="inputFileName" format="bed" type="data" label="Input File"/>
			</when>
			<when value="gff">
				<param name="inputFileName" format="gff" type="data" label="Input File"/>
			</when>
			<when value="gff2">
				<param name="inputFileName" format="gff2" type="data" label="Input File"/>
			</when>
			<when value="gff3">
				<param name="inputFileName" format="gff3" type="data" label="Input File"/>
			</when>
			<when value="sam">
				<param name="inputFileName" format="sam" type="data" label="Input File"/>
			</when>
			<when value="gtf">
				<param name="inputFileName" format="gtf" type="data" label="Input File"/>
			</when>
		</conditional>
  </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>