IntaRNA
            ## Multithreading
                --threads "\${GALAXY_SLOTS:-1}"
            ## basic general parameters
                ## Query parameters
                --query '$advancedOptions.query.query'
                --qAcc $advancedOptions.query.qAcc_cond.qAcc
                #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
                    --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
                #end if
                --qAccW $advancedOptions.query.qAccW
                --qAccL $advancedOptions.query.qAccL
                ## Target param.
                --target '$advancedOptions.target.target'
                --tAcc $advancedOptions.target.tAcc_cond.tAcc
                #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"
                    --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
                #end if
                --tAccW $advancedOptions.target.tAccW
                --tAccL $advancedOptions.target.tAccL
                ## Seed param.
                #if $advancedOptions.seed.noSeed
                    $advancedOptions.seed.noSeed
                #else
                    --seedBP $advancedOptions.seed.seedBP
                    #if $advancedOptions.seed.seedMaxUP > 0
                        --seedMaxUP $advancedOptions.seed.seedMaxUP
                    #end if
                #end if
                ## Prediction param.
                --mode $advancedOptions.interaction.mode
                --energy V
                ## Output param.
                --out $outfile
                --outMode C
                --outSep "`printf "\t"`"
                --outNumber $advancedOptions.output.outNumber
                --outOverlap $advancedOptions.output.outOverlap
                --outCsvCols '$advancedOptions.output.outCsvCols'
                --outCsvSort '$advancedOptions.output.outCsvSort'
                $advancedOptions.output.outPairwise
            #if $advancedOptions.advancedSelector == "advanced"
                ## Query parameters
                --qIntLoopMax $advancedOptions.query.qIntLoopMax
                #if $advancedOptions.query.qRegion
                    --qRegion '$advancedOptions.query.qRegion'
                #end if
                ## Target param.
                --tIntLoopMax $advancedOptions.target.tIntLoopMax
                #if $advancedOptions.target.tRegion
                    --tRegion '$advancedOptions.target.tRegion'
                #end if
                ## Seed param.
                #if not $advancedOptions.seed.noSeed
                    --seedMaxE $advancedOptions.seed.seedMaxE
                    --seedMinPu $advancedOptions.seed.seedMinPu
                    #if $advancedOptions.seed.seedQMaxUP
                        --seedQMaxUP $advancedOptions.seed.seedQMaxUP
                    #end if
                    #if $advancedOptions.seed.seedTMaxUP
                        --seedTMaxUP $advancedOptions.seed.seedTMaxUP
                    #end if
                    #if $advancedOptions.seed.seedQRange
                        --seedQRange '$advancedOptions.seed.seedQRange'
                    #end if
                    #if $advancedOptions.seed.seedTRange
                        --seedTRange '$advancedOptions.seed.seedTRange'
                    #end if
                #end if
                ## SHAPE param.
                #if $advancedOptions.shape.qShape
                    --qShape '$advancedOptions.shape.qShape'
                #end if
                #if $advancedOptions.shape.tShape
                    --tShape '$advancedOptions.shape.tShape'
                #end if
                ## Prediction param.
                --model $advancedOptions.interaction.model
                --energyVRNA '$advancedOptions.interaction.energyVRNA'
                --temperature $advancedOptions.interaction.temperature
                #if $advancedOptions.interaction.windowWidth
                    --windowWidth $advancedOptions.interaction.windowWidth
                    --windowOverlap $advancedOptions.interaction.windowOverlap
                #end if
                ##Output param.
                --outMaxE $advancedOptions.output.outMaxE
                --outDeltaE $advancedOptions.output.outDeltaE
                ## add additional output files
                #if $advancedOptions.output.add_output_cond.selector == "add"
                  #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'
                    #for $outFile in $advancedOptions.output.add_output_cond.add_output.value:
                      #if $outFile == 'qAcc' or $outFile == 'tAcc'
                        #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.led'
                      #else
                      #if $outFile == 'qAcc' or $outFile == 'tAcc' or $outFile == 'qPu' or $outFile == 'tPu'
                        #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.lpu'
                      #else
                        #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.tabular'
                      #end if
                      #end if
                      --out '$curOutFile'
                    #end for
                  #end if
                #end if
            #end if