<tool id="prepareAnnotation" name="prepare annotation file">
  <description>Prepares Annotation file -> clusterizes, filters exon and sorts annotations.</description>
  <command interpreter="bash"> prepareAnnot.sh $inputFile $outputFile  </command>
  <inputs>
    <param name="inputFile" type="data" label="Input File" format="gff"/>
  </inputs>

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

  <help>
	command example: sh prepareAnnot.sh NC_011744r_annot_tmp1.gff NC_011744r_annot_pre1.gff
  </help>
</tool>