RNAalifold  < '$input' > '$tabularFile'
        
        #if $input.ext == 'clustal':
            -f C
        #else if $input.ext == 'fasta':
            -f F
        #else if $input.ext == 'stockholm':
            -f S
        #else if $input.ext == 'maf':
            -f M
        #else:
            -f C
        #end if
        -T$model_options.temperature -d$model_options.dangling
        $general_options.verbose
        $general_options.color
        $general_options.alignment
        #if $general_options.layout_type ==0
            --layout-type=$general_options.layout_type
        #end if
        $general_options.noPS
        #if str($IDs.id_prefix) <> "alignment"
            --id-prefix='$IDs.id_prefix'
        #end if
        $IDs.continuous_ids
        $IDs.auto_id
        #if $IDs.id_digits <> 4
            --id-digits=$IDs.id_digits
        #end if
        #if $IDs.id_start <> 1
            --id-start=$IDs.id_start
        #end if
        #if $constraints.maxBPspan <> -1
            --maxBPspan=$constraints.maxBPspan
        #end if
        #if str($constraints.constraintLocation.constraintSelector) == "fromFile"
            --constraint='$constraints.constraintLocation.constraintsFile'
            $constraints.constraintLocation.batch
            $constraints.ss_cons
        #end if        
        #if str($constraints.shapeOption.shapeSelector) == "isUsed"
            #if len($constraints.shapeOption.shape_files) > 0
                #set $sf=list()
                #for $i in $constraints.shapeOption.shape_files
                    $sf.append(str('$i.shape'))
                #end for
                --shape= #echo ','.join($sf)
                #if $constraints.shapeOption.m <> 1.8 or  $constraints.shapeOption.b <> -0.6
                    #set $s="Dm"+str($constraints.shapeOption.m)+"b"+str($constraints.shapeOption.b)
                    --shapeMethod=$s
                #end if		
            #end if
        #end if

        #if $algorithm_options.pf <> "-1"
            --partfunc=$algorithm_options.pf
            --pfScale=$algorithm_options.pfScale

        #end if
        #if $algorithm_options.measelect.mea == "yes":
            --MEA=$algorithm_options.measelect.meavalue
            --pfScale=$algorithm_options.pfScale
        #end if

        $algorithm_options.mis
        #if $algorithm_options.stochBT_en <> 1
            --stochBT_en=$algorithm_options.stochBT_en
        #end if
        $algorithm_options.circular
        #if $algorithm_options.bppmThreshold <> 1e-6
            --bppmThreshold=$algorithm_options.bppmThreshold
        #end if
        $algorithm_options.gquad
        $algorithm_options.sci		
        $model_options.notetra
        $model_options.nolp
        $model_options.nogu
        $model_options.noclosinggu
        #if $model_options.cfactor <> 1.0
            --cfactor=$model_options.cfactor
        #end if
        #if $model_options.nfactor <> 1.0
            --nfactor=$model_options.nfactor
        #end if
        $model_options.endgaps
        $model_options.ribosum
        #if $model_options.nsp
            --nsp='$model_options.nsp'
        #end if
        #if $model_options.betaScale <> 1.0
            --betaScale=$model_options.betaScale
        #end if
        && tar -cf '$imagesFile' *.ps