ln -s '$input_cnr_file' ./tumor.cnr &&
        #if $advanced_settings.segment
        ln -s '$advanced_settings.segment' ./segment.cns &&
        #end if
        #if $advanced_settings.range_list
            ln -s '$advanced_settings.range_list' ./list.bed &&
        #end if
        #if $advanced_settings.additional_SNP_allelic_process.vcf
            ln -s '$advanced_settings.additional_SNP_allelic_process.vcf' ./vcf_file.vcf &&
        #end if
        cnvkit.py scatter
            ./tumor.cnr
            --output sample-scatter.pdf
            #if $advanced_settings.segment
                --segment ./segment.cns
            #end if
            #if $advanced_settings.chromosome
                --chromosome '$advanced_settings.chromosome'
            #end if
            #if $advanced_settings.gene
                --gene '$advanced_settings.gene'
            #end if
            #if $advanced_settings.range_list
                --range-list ./list.bed
            #end if
            #if str($advanced_settings.width)
                --width  $advanced_settings.width
            #end if
            #if $advanced_settings.plot_aesthetics.antitarget_marker
                --antitarget-marker '$advanced_settings.plot_aesthetics.antitarget_marker'
            #end if
            $advanced_settings.plot_aesthetics.by_bin
            #if $advanced_settings.plot_aesthetics.segment_color
                --segment-color '$advanced_settings.plot_aesthetics.segment_color'
            #end if
            #if $advanced_settings.plot_aesthetics.title
                --title '$advanced_settings.plot_aesthetics.title'
            #end if
            $advanced_settings.plot_aesthetics.trend
            #if str($advanced_settings.plot_aesthetics.y_max)
                --y-max $advanced_settings.plot_aesthetics.y_max
            #end if
            #if str($advanced_settings.plot_aesthetics.y_min)
                --y-min $advanced_settings.plot_aesthetics.y_min
            #end if
            #if str($advanced_settings.plot_aesthetics.fig_size)
                --fig-size $advanced_settings.plot_aesthetics.fig_size
            #end if
            #if $advanced_settings.additional_SNP_allelic_process.vcf
                --vcf ./vcf_file.vcf
            #end if
            #if $advanced_settings.additional_SNP_allelic_process.sample_id
                --sample-id '$advanced_settings.additional_SNP_allelic_process.sample_id'
            #end if
            #if $advanced_settings.additional_SNP_allelic_process.normal_id
                --normal-id '$advanced_settings.additional_SNP_allelic_process.normal_id'
            #end if
            #if str($advanced_settings.additional_SNP_allelic_process.min_variant_depth)
                --min-variant-depth $advanced_settings.additional_SNP_allelic_process.min_variant_depth
            #end if
            #if str($advanced_settings.additional_SNP_allelic_process.zygosity_freq)
                --zygosity-freq $advanced_settings.additional_SNP_allelic_process.zygosity_freq
            #end if