<tool id="ConvertTranscriptFile_SamToGff2" name="Sam -> Gff2">
  <description>Convert Sam File to Gff2 File.</description>
  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f sam -o $outputFile -g gff2 yes 2>$logFile </command>
  <inputs>
    <param name="inputFile" type="data" label="Input File" format="sam"/>
  </inputs>

  <outputs>
    <data format="gff" name="outputFile" label="[sam -> gff2] Output File"/>
    <data format="txt" name="logFile" label="[sam -> gff2] Log File"/>
  </outputs>

  <help>
  </help>
</tool>