ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
    hicAggregateContacts
    --matrix 'matrix.$matrix_h5_cooler.ext'
    --BED '$BED'
    #if $BED2:
        --BED2 '$BED2'
    #end if

    --range '$range_min:$range_max'
    --numberOfBins '$numberOfBins'

    --transform $transform
    --operationType $operationType
    --mode $mode
    $row_wise
    $perChr
    --largeRegionsOperation $largeRegionsOperation
    #if $outputs and 'PrefixMatrix' in $outputs:
        --outFilePrefixMatrix 'matrix_values'
    #end if

    #if $outputs and 'outFileContactPairs' in $outputs:
        --outFileContactPairs 'contact_positions'
    #end if

    #if $outputs and 'HeatmapFile' in $outputs:
        --diagnosticHeatmapFile 'heatmap'
    #end if

    #if $outputs and 'outFileObsExp' in $outputs:
        --outFileObsExp 'ObsExp.$matrix_h5_cooler.ext'
    #end if

    #if $clustering:
        $clustering
    #end if

    #if $howToCluster:
        --howToCluster $howToCluster
    #end if

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

    #if $plotType:
        --plotType $plotType
    #end if

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

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

    #if $vMax:
        --vMax $vMax
    #end if
 
    $considerStrandDirection
 
    --outFileName plot.$image_file_format
    &&
    mv plot.$image_file_format plot
    #if $outputs and 'outFileObsExp' in $outputs:
        && mv 'ObsExp.$matrix_h5_cooler.ext' matrix
    #end if