<tool id="CountReadGCPercent" name="count read GC percent">
    <description>Count GC percent for each read against a genome.</description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
    <command interpreter="python"> ../Java/Python/CountReadGCPercent.py -i $inputFastaFile -j $inputGffFile -o $outputFile</command>
  <inputs>
      <param name="inputFastaFile" type="data" label="Input reference fasta File" format="fasta"/>
      <param name="inputGffFile" type="data" label="Input File" format="gff3"/>
  </inputs>

  <outputs>
    <data format="gff3" name="outputFile" label="[count read GC percent] Output File"/>
   </outputs>

  <help>
Count the GC% of a FASTA file.
  </help>
</tool>