<tool id="coverageGff" name="coverage Gff">
  <description>Computes reads coverage form a "nbElements" tag and writes the calculated coverage in a gff3 out file.</description>
  <command interpreter="perl"> coverageGff.pl -i $inputFile -l $readSize > $outputFile  </command>
  <inputs>
    <param name="inputFile" type="data" label="Input File" format="gff"/>
    <param name="readSize" type="integer" value="38" help="The size of read, default: 38nt"/>

  </inputs>

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

  <help>
	command example: perl coverageGff.pl -i *_trans_inIG.gff > *_trans_inIG_cov.gff
  </help>
</tool>