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<tool id="export2sam" name="Export to SAM" version="0.1">
  <description></description>
  <parallelism method="basic"></parallelism>
  <command interpreter="sh">
    export2sam.sh
      -a $read1
      #if $pairCondition.pairSelect == "yes"
        -b $read2
      #end if
      -o $output
      $gunzip
      $remove
  </command>
  <inputs>
    <param name="read1" type="data" format="eland_export" label="ELAND export file" help="" />
    <param name="gunzip" type="boolean" truevalue="-g" falsevalue="" checked="True" label="Input file is gzipped" help="" />
    <param name="remove" type="boolean" truevalue="-r" falsevalue="" checked="True" label="Remove (chr).fa and chr_fragments.fa/" help="" />
    <conditional name="pairCondition">
      <param name="pairSelect" type="select" label="Pair end?">
        <option value="yes">Yes</option>
        <option value="no" selected="True">No</option>
      </param>
      <when value="yes">
        <param name="read2" type="data" format="eland_export" label="ELAND export file" help="" />
      </when>
      <when value="no"></when>
    </conditional>
  </inputs>
  <outputs>
    <data format="sam" name="output" label="${tool.name} on ${on_string}"/>
  </outputs>
  <help>If thou thyself canst do it, attend no other's help or hand.</help>
</tool>