#import re

        mkdir output &&
        #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
            ln -s '$m' '${counter}_matrix.$m.ext' &&
        #end for
        #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
        #set $m_out = ' '.join([ "'output/%s_norm_%s'" % ($counter, re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])

        hicNormalize --matrices $m
        #if $normalize_conditional.normalize == 'multiplicative':
            --multiplicativeValue $normalize_conditional.multiplicativeValue
        #end if
        --normalize $normalize_conditional.normalize
        #if $zero_threshold_value:
            --setToZeroThreshold $zero_threshold_value
        #end if

        --outFileName $m_out