#if str($source.source_selector) == "advanced":
        paste
        #set $start = True
        #set $header = ''
        #for $time in $source.rep_time:
            #for $file in $time.files:
                #if $start:
                    <(cut -f1 $file)
                    #set $start = False
                #end if
                #set $header += ' "' + $file.name + '"'
                <(cut -f2 $file)
            #end for
        #end for
        > data && sed -i '1i$header' data &&
        #if $source.enable_output:
            cp $design_matrix $edesign_out &&
        #end if
        #set $data = 'data'
        #set $edesign = $design_matrix
    #else:
        #set $data = $source.data
        #set $edesign = $source.edesign
    #end if
    Rscript '${__tool_directory__}/masigpro.R'
    -e '$edesign'
    -d '$data'
    -o '$masigpro_out'
    #if str($source.source_selector) == "defaults":
        --time_col $source.time_col
        --repl_col $source.repl_col
    #end if
    --degree $makeDesignMatrix.degree
    --qvalue $p_vector.qvalue
    --min_obs $p_vector.min_obs
    --step_method '$Tfit.step_method'
    --nvar_correction $Tfit.nvar_correction
    --alfa $Tfit.alfa
    --rsq $getSiggenes.rsq
    --vars '$getSiggenes.vars'
    --significant_intercept '$getSiggenes.significant_intercept'
    #if $pdf.pdf_selector:
        --cluster_data $pdf.seeGenes.clusterData
        -k $pdf.seeGenes.k
        --print_cluster $pdf.seeGenes.print_cluster
        --cluster_method $pdf.seeGenes.clustering.clusterMethod
        #if str($pdf.seeGenes.clustering.clusterMethod) == "hclust":
            --distance $pdf.seeGenes.clustering.distance
            --agglo_method $pdf.seeGenes.clustering.aggloMethod
        #end if
        #if str($pdf.seeGenes.clustering.clusterMethod) == "kmeans":
            --iter_max $pdf.seeGenes.clustering.iterMax
        #end if
        --color_mode $pdf.seeGenes.colorMode
        --show_fit $pdf.seeGenes.showFit
        --show_lines $pdf.seeGenes.showLines
        --cexlab $pdf.seeGenes.cexlab
        --legend $pdf.seeGenes.legend
    #end if
    #if str($source.source_selector) == "advanced" and $source.enable_output
        && mv data $data_out
    #end if