<tool id="cleanGff" name="clean Gff">
	  <description>Cleans a GFF file as given by NCBI and outpus a Gff3 file.</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="tag option, compulsory option" help="lists of comma separated types that you want to keep.EX: ncRNA,tRNA,rRNA,CDS"/>
	      </inputs>

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

</tool>