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

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

  <help>
  </help>
</tool>