<tool id="changeGffFeatures" name="change GFF features">
	<description>Change a feature in a GFF file (the feature is the 3rd column).</description>
		<requirements>
			<requirement type="set_environment">PYTHONPATH</requirement>
		</requirements>
		<command interpreter="bash">
			../Java/Python/changeGffFeatures.sh $inputFile $inputFeature $outputFeature >$outputFile
		</command>
      <inputs>
	      <param name="inputFile" type="data" label="Input File" format="gff"/>	
	      <param name="inputFeature" type="text" value="exon" label="The feature you want to change"/>
	      <param name="outputFeature" type="text" value="exon" label="The new feature"/>
      </inputs>

      <outputs>
             <data name="outputFile" format="gff" label="[change GFF features] Output File"/>
      </outputs> 

	  <help>
		This script changes the third column of a GFF3 file (please refer to http://www.sequenceontology.org/gff3.shtml to know more about this format).
	  </help>
</tool>