<tool id="cleanGff" name="clean Gff">
	  <description>Clean a GFF file (e.g. as given by NCBI) and produces a new GFF3 file, understood by S-MART.</description>
	  <command interpreter="python"> ../Java/Python/cleanGff.py -i $inputFile 
		  -t $type 
		  -o $outputFile
	  </command>

	      <inputs>
		      <param name="inputFile" type="data" label="Input File" format="gff"/>
		      <param name="type" type="text" value="tRNA,rRNA,ncRNA,CDS" label="Tags you keep" help="lists of comma separated types that you want to keep, e.g. ncRNA,tRNA,rRNA,CDS"/>
	      </inputs>

	      <outputs>
	          <data format="gff3" name="outputFile" label="[cleanGff] Output File"/>
	      </outputs>

	<help>
		A GFF file (please consult http://www.sequenceontology.org/gff3.shtml to know more about it) may contain different sources of information: chromosome size, genes, transcripts, etc. S-MART mostly works on transcripts. This scripts filters the input GFF3 to keep the information you really want, based on the feature (3rd column).
	</help>
</tool>