ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
        hicDetectLoops

            --matrix  'matrix.$matrix_h5_cooler.ext'
            #if $peakWidth:
                --peakWidth $peakWidth
            #end if

            #if $windowSize:
                --windowSize $windowSize
            #end if

            #if $pValuePreselection:
                --pValuePreselection $pValuePreselection
            #end if

            #if $peakInteractionsThreshold:
                --peakInteractionsThreshold $peakInteractionsThreshold
            #end if

            #if $obsExpThreshold:
                --obsExpThreshold $obsExpThreshold
            #end if
           
            #if $pValue:
                --pValue $pValue
            #end if
            #if $maxLoopDistance:
                --maxLoopDistance $maxLoopDistance
            #end if

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

            #if $chromosomes:
                #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
                --chromosomes $chromosome
            #end if

            --expected $expected
            --outFileName output_loop.bedgraph
            --threads \${GALAXY_SLOTS:-4} -tpc \${GALAXY_SLOTS:-4}