#if $function.function_select == "base": 
        Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/Seurat.R\",
        params = list(counts = \"${function.input}\",
        min_cells = \"${function.min_cells}\",
        min_genes = \"${function.min_genes}\",
        low_thresholds = \"${function.low_thresholds}\",
        high_thresholds = \"${function.high_thresholds}\",
        vlnfeat = \"${function.vlnfeat}\",
        norm_out = \"${function.norm_file}\",
        #if $function.variable_continue.variable_continue == "yes":
            featplot = \"${function.variable_continue.featplot}\",
            variable_out = \"${function.variable_continue.var_file}\",
            #if $function.variable_continue.pca_continue.pca_continue == "yes":
                numPCs = \"${function.variable_continue.pca_continue.num_PCs}\",
                PCplots = \"${function.variable_continue.pca_continue.pc_plots}\",
                pca_out = \"${function.variable_continue.pca_continue.pca_file}\",
                #if $function.variable_continue.pca_continue.clusters_continue.clusters_continue == "yes":
                    perplexity = \"${function.variable_continue.pca_continue.clusters_continue.perplexity}\",
                    resolution = \"${function.variable_continue.pca_continue.clusters_continue.resolution}\",
                    nmds = \"${function.variable_continue.pca_continue.clusters_continue.nmds}\",
                    clusters_out = \"${function.variable_continue.pca_continue.clusters_continue.clusters_file}\",
                    #if $function.variable_continue.pca_continue.clusters_continue.markers_continue.markers_continue == "yes":
                        min_pct = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.min_pct}\",
                        logfc_threshold = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.logfc_threshold}\",
                        heatmaps = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.heatmaps}\",
                        markers_out = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.markers_file}\",
                        end_step="\"5"\",
                    #else:
                        end_step="\"4"\",
                    #end if
                #else:
                    end_step="\"3"\",
                #end if
            #else:
                end_step="\"2"\",
            #end if
        #else:
            end_step="\"1"\",
        #end if
        varstate = \"${meta.varstate}\",
        warn = \"${meta.warn}\",
        showcode = \"${meta.showcode}\"),
        intermediates_dir = \".\",
        output_format = html_document(),
        output_dir = \".\",
        output_file = \"out.html\")"
    #else:
        Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/citeseq_Seurat.R\",
        params = list(rna = \"${function.rna}\",
        prot = \"${function.prot}\",
        cite_markers = \"${function.cite_markers}\",


        #if $function.comparison.comparison == "yes"
            comparison="\"T"\",
            feat_comp=\"${function.comparison.feat_comp}\",
        #else:
            comparison="\"F"\",
            feat_comp="\""\",
        #end if
        #if $function.marker_compare.marker_compare == "yes"
            marker_compare="\"T"\",
            top_x=\"${function.marker_compare.top_x}\",
        #else:
            marker_compare="\"F"\",
            top_x="\""\",
        #end if
        min_cells = \"${function.min_cells}\",
        min_genes = \"${function.min_genes}\",
        low_thresholds = \"${function.low_thresholds}\",
        high_thresholds = \"${function.high_thresholds}\",
        vlnfeat = \"${function.vlnfeat}\",
        norm_out = \"${function.norm_file}\",
        featplot = \"${function.featplot}\",
        variable_out = \"${function.var_file}\",
        numPCs = \"${function.num_PCs}\",
        PCplots = \"${function.pc_plots}\",
        pca_out = \"${function.pca_file}\",
        perplexity = \"${function.perplexity}\",
        resolution = \"${function.resolution}\",
        nmds = \"${function.nmds}\",
        clusters_out = \"${function.clusters_file}\",
        min_pct = \"${function.min_pct}\",
        logfc_threshold = \"${function.logfc_threshold}\",
        heatmaps = \"${function.heatmaps}\",
        markers_out = \"${function.markers_file}\",
        varstate = \"${meta.varstate}\",
        warn = \"${meta.warn}\",
        showcode = \"${meta.showcode}\"),
        intermediates_dir = \".\",
        output_format = html_document(),
        output_dir = \".\",
        output_file = \"out.html\")"
    #end if