#set $matrices = []
        #set $mlabels = []
        #for $counter, $i in enumerate($input_files):
            ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext'; 
            #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter,  $i.matrix.ext))

            #if str($i.mlabel.value) != "":
                #set $mlabels += ['\'%s\'' % ($i.mlabel.value)]
            #else
                #set $mlabels += ['\'%s\'' % ($i.matrix.name)]
            #end if
        #end for
        #set $mlabels = ' '.join($mlabels)
        #set $matrices = ' '.join($matrices)
    
        hicCorrelate

            --matrices $matrices
            --labels $mlabels

            #if $method and $method is not None:
                --method $method
            #end if
            $log1p

            
        #if $use_range.select_use_range == "yes_use_range":
            --range $use_range.range_min:$use_range.range_max
        #end if
    

            #if $chromosomes:
                --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])#
            #end if

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

            --outFileNameHeatmap heatmap.png
            --outFileNameScatter scatter.png