Rscript '$__tool_directory__/plotwithscale.R' adjustedpvalue='${adjustedpvalue}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}'
      iwtomicsrdata='${rdata}'
      iwtomicstests='${testids}'
      iwtomicsselectedfeatures='${featureids}'

      #set test_subset = '|'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )
      test_subset='${test_subset}'
      #set feature_subset = '|'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )
      feature_subset='${feature_subset}'
      #set scale_subset = ','.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )
      scale_subset='c(${scale_subset})'

      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