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

        
        #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
    

        --outputFileName pca1.$outputFormat pca2.$outputFormat
        --format $outputFormat

        #if $ligation_factor:
            $ligation_factor
        #end if

        #if $ignoreMaskedBins:
            $ignoreMaskedBins
        #end if

        #if $extra_track_conditional.extra_track_selection == 'gene_density':
            --extraTrack '$extra_track_conditional.extraTrack'
        #elif $extra_track_conditional.extra_track_selection == 'histon_mark':
            --extraTrack '$extra_track_conditional.extraTrack'
            --histonMarkType '$extra_track_conditional.histonMarkType'
        #end if

        #if $pearsonMatrix:
            --pearsonMatrix pearson.$matrix_h5_cooler.ext
        #end if

        #if $obsexpMatrix:
            --obsexpMatrix obsexp.$matrix_h5_cooler.ext
        #end if

        && mv pca1.$outputFormat pca1
        && mv pca2.$outputFormat pca2
        #if $pearsonMatrix:
            && mv pearson.$matrix_h5_cooler.ext pearson
        #end if

        #if $obsexpMatrix:
            && mv obsexp.$matrix_h5_cooler.ext obsexp
        #end if