<tool id="DESEQ" name="DESEQ for differential expression analysis">
  <description>Differential expression analysis for reads count data</description>
  <command interpreter="bash"> deseq.sh $inputFile $header $withOutReplicates $outHTML $outHTML.files_path $outComplete $outUP $outDown 2> $log </command>

  <inputs>
      <param name="inputFile" type="data" label="Input File list" format="txt"/>
      <param name="header" type="boolean" truevalue="1" falsevalue="0" checked="false" label="If there is a header for your count files, please choose this case."/>
      <param name="withOutReplicates" type="boolean" truevalue="1" falsevalue="0" checked="false" label="If your data has not replicates, please choose this case."/>

  </inputs>

  <outputs>
      <data format="HTML" name="outHTML" label="[DESEQ] Output HTML File" help="This output file shows all results images by DESeq analysis"/> 
      <data format="tabular" name="outComplete" label="[DESEQ] Output complete File"/> 
      <data format="tabular" name="outUP" label="[DESEQ] Output up File" help="This output file shows the genes of group1 which are overexpressed than those of group2"/> 
      <data format="tabular" name="outDown" label="[DESEQ] Output down File" help="This output file shows the  genes of group1 which are less expressed than those of group2"/>
      <data format="txt" name="log" label="[DESEQ] Output log File"/> 
  </outputs>

  <help>
  </help>
</tool>