<tool id="rankprodthree" name="RankProd" >
 <requirements>
     <container type="docker">bianca7/lncrna:rankprod</container>
 </requirements>
 <description>Differential expression with RankProd</description>
 <stdio>
   <exit_code range="1:" level="fatal" />
 </stdio>
 <command><![CDATA[
       #if $choose.genes=='T'
      Rscript /logrankprod.R "c($whichcols)" $file1 "c($whichrows)" $sc $file2 $file3 $norm $base $log $choose.genes $choose.numgenes
     #end if
     #if $choose.genes=='F'
      Rscript /logrankprod.R "c($whichcols)" $file1 "c($whichrows)" $sc $file2 $file3 $norm $base $log $choose.genes $choose.method $choose.cutoff
     #end if
  ]]></command>
  <inputs>
   <param format="tabular, txt" name="file1" type="data" label="input matrix" />
   <param name="whichcols" type="text" label="Comma separated fields for columns, like 1,2,3,4" />
   <param name="sc" type="integer" value="1" label="Choose col class" />
   <param format="tabular, txt" name="file2" type="data" label="input samples matrix" />
   <param name="whichrows" type="text" label="Comma separated fields for rows" />
   <param name="norm" type="boolean" truevalue="T" falsevalue="F" selected="FALSE" label="Are counts normalized?" />
   <param name="base" type="select" label="Choose log base" >
     <option value="2">2</option>
     <option value="10">10</option>
   </param>
   <param name="log" type="boolean" truevalue="T" falsevalue="F" selected="FALSE" label="Are they logarithmically transformed?" />
   <conditional name="choose" >
     <param name="genes" type="boolean" truevalue="T" falsevalue="F" checked="no" label="Select specific genes or choose method" />
     <when value="T">
       <param name="numgenes" type="integer" value="10" label="How many genes" />
     </when>
     <when value="F">
       <param name="method" type="select" label="Select method" >
        <option value="pfp">pfp</option>
        <option value="pval">pval</option>
       </param>
       <param name="cutoff" type="float" value="0.05" label="Choose cutoff" />
     </when>
   </conditional>
 </inputs>
 <outputs>
    <data format="txt" name="file3" label="Differentially expressed molecules"/>
 </outputs>
</tool>