<tool id="stingray_Flash" name="Flash">
  <description>Flash</description>

  <command interpreter="ruby">Flash_wrapper.rb $sequence1 $sequence2 $readLen $fragLen $maxOverlap $extended $not1 $not2</command>

  <inputs>
    <param format="fastq" name="sequence1" type="data" label=""/>
    <param format="fastq" name="sequence2" type="data" label=""/>
    <param name="readLen" size="10" type="text" value="100">
      <label>Average read length</label>
    </param>
    <param name="fragLen" size="10" type="text" value="180">
      <label>Fragment length</label>
    </param>
   <param name="maxOverlap" size="10" type="text" value="70">
      <label>Maximum overlap length</label>
    </param>


  </inputs>

  <outputs>
    <data format="fastq" name="not1" label="NotCombined1"/>
    <data format="fastq" name="not2" label="NotCombined2"/>
    <data format="fastq" name="extended" label="Combined Reads"/>
  </outputs>

  <tests>
    <test>
    </test>
  </tests>

  <help>
  </help>

</tool>