Rscript '$__tool_directory__/testandplot.R' adjustedpvaluematrix='${adjustedpvaluematrix}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}' iwtomicsrdata='${iwtomicsrdata}' iwtomicstests='${iwtomicstests}' iwtomicsselectedfeatures='${iwtomicsselectedfeatures}'
      regionids='${regionids}'
      featureids='${featureids}'
      rdatafile='${rdata}'

      #set region1 = ','.join( [ str( $r.region0 ) for $r in $regionssection.regions ] )
      #set region2 = ','.join( [ str( $r.region1 ) for $r in $regionssection.regions ] )
      region1='c(${region1})'
      region2='c(${region2})'

      features_subset='c(${featureslist})'

      statistics="'${conditionalstatistics.statistics}'"
      #if $conditionalstatistics.statistics == "quantile":
        #set probabilities = ','.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] )
        testprobs='c(${probabilities})'
      #end if

      B='${permutations}'

      testalpha='${plotres.alpha}'
      average='${plotres.average}'
      size='${plotres.size}'
      plottype="'${plotres.conditionalplottype.plottype}'"
      #if $plotres.conditionalplottype.plottype == "boxplot":
        #set probs = ','.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
        #if $probs != "":
          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})'
        #else:
          probs='c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})'
        #end if
      #end if

      groupby="'${plotsum.conditionalgroupby.groupby}'"
      #if $plotsum.conditionalgroupby.groupby == "test":
        summaryalpha='${plotsum.conditionalgroupby.testalphaplot}'
        only_significant='${plotsum.conditionalgroupby.testonlysig}'
      #elif $plotsum.conditionalgroupby.groupby == "feature":
        summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
        only_significant='${plotsum.conditionalgroupby.featureonlysig}'
      #end if