#import re

        #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
            #set identifier = re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))
            ln -s '$m' '${counter}_$identifier' &&
        #end for
        #set $m = ' '.join([ '\'%s_%s\'' % ($counter, re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])

        hicPlotSVL
            --matrices $m
            #if $distance:
                --distance $distance
            #end if

            
        #if $chromosome_list:
            #set $chromosomes = []
            #for $chrom in $chromosome_list:
                #silent $chromosomes.append("'%s'" % $chrom.chromosomes)
            #end for
            #set $chromosome_string = ' '.join($chromosomes)
            --chromosomes $chromosome_string
        #end if
    

            #if $colorList:
                #set $colorList_new = ' '.join([ '\'%s\'' % $color for $color in str($colorList).split(' ') ])
                --colorList $colorList_new
            #end if

            #if $dpi:
                --dpi $dpi
            #end if
            --plotFileName plot.$image_file_format
            --outFileName p_values.txt
            --outFileNameData ratios.txt
            --threads \${GALAXY_SLOTS:-4}

            && mv plot.$image_file_format plot