<tool id="testDiffExpAnal" name="Differential Expression Analysis">
  <description>Differential expression analysis for sequence count data (DESeq)</description>
  <command interpreter="sh"> ../DiffExpAnal/testR.sh $inputFile $columnsOfGeneName $columnsOfCondition1 $columnsOfCondition2 $outputFileCSV $outputFilePNG 2>$outputLog </command>
  <inputs>
    <param name="inputFile" type="data" label="Input File" format="tabular"/>
	<param name="columnsOfGeneName" type="text" value="0" label="Please indicate the column numbers of gene names with ',' separator. If There are not gene names, default value is 0."/>
	<param name="columnsOfCondition1" type="text" value="1,2" label="Please indicate the column numbers of condition1 with ',' separator."/>
	<param name="columnsOfCondition2" type="text" value="3,4" label="Please indicate the column numbers of condition2 with ',' separator."/>
  </inputs>

  <outputs>
    <data format="tabular" name="outputFileCSV" label="[DiffExpAnal] Output CSV File"/>
	<data format="png" name="outputFilePNG" label="[DiffExpAnal] Output PNG File"/>
    <data format="tabular" name="outputLog" label="[DiffExpAnal] Log File"/>
  </outputs>

  <help>
  </help>
</tool>