#if str($pca_conditional.pca_type) == 'bigwig':
            ln -s '$pca_conditional.pca_bigwig' pca.bw &&
            #set $pca = '--bigwig pca.bw'
        #elif str($pca_conditional.pca_type) == 'no_file':
            #set $pca = ''
        #end if
        ln -s $matrix_h5_cooler matrix.$matrix_h5_cooler.ext &&
        hicPlotMatrix
            --matrix 'matrix.$matrix_h5_cooler.ext'

            #if $title and $title is not None:
                --title '$title'
            #end if

            #if $scoreName and $scoreName is not None:
                --scoreName '$scoreName'
            #end if

            --outFileName plot.$image_file_format

            $perChromosome
            $clearMaskedBins

            ## special: --chromosomeOrder is optional, but if given needs at least one argument
            #set chroms = ' '.join([ '\'' + str($var.chromosome) + '\'' for $var in $chromosomeOrder ])
            #if chroms:
                --chromosomeOrder $chroms
            #end if

            #if $region:
                --region '$region'
            #end if

            #if $region2:
                --region2 '$region2'
            #end if
            $log1p
            $log

            #if $colormap:
                --colorMap $colormap
            #end if

            #if $vMin:
                --vMin $vMin
            #end if

            #if $vMax:
                --vMax $vMax
            #end if

            #if str($pca_conditional.pca_type) == 'bigwig':
                #if $pca_conditional.vMinBigwig:
                    --vMinBigwig $pca_conditional.vMinBigwig
                #end if
                #if $pca_conditional.vMaxBigwig:
                    --vMaxBigwig $pca_conditional.vMaxBigwig
                #end if
                $pca_conditional.flipBigwigSign

                #if $pca_conditional.scaleFactorBigwig:
                    --scaleFactorBigwig $pca_conditional.scaleFactorBigwig
                #end if
                $pca_conditional.bigwigAdditionalVerticalAxis
            #end if
            $pca
            #if $dpi:
                --dpi $dpi
            #end if

            #if $fontSize:
                --fontSize $fontSize
            #end if

            #if $rotationX:
                --rotationX $rotationX
            #end if

            #if $rotationY:
                --rotationY $rotationY
            #end if

            #if $increaseFigureWidth:
                --increaseFigureWidth $increaseFigureWidth
            #end if

            #if $increaseFigureHeight:
                --increaseFigureHeight $increaseFigureHeight
            #end if

            #if str($loop_conditional.loop_selector) == 'yes':
                    --loops $loop_conditional.loops
                    --loopLargeRegionsOperation $loop_conditional.loops_large_selector
            #end if

            #if $tads:
                --tads '$tads'
            #end if
        && mv plot.$image_file_format plot