#if str($reference.source) == "history":
            #set $ref_genome = 'ref.fa'
            ln -s -f '$reference.genome' $ref_genome &&
        #else:
            #set $ref_genome = str($reference.genome.fields.path)
        #end if
        #set $normal_data = 'normal.bam'
        #set $tumor_data = 'tumor.bam'
        ln -s -f '$normal_bam' $normal_data &&
        ln -s -f '$tumor_bam' $tumor_data &&
        ln -s -f '${normal_bam.metadata.bam_index}' ${normal_data}.bai &&
        ln -s -f '${tumor_bam.metadata.bam_index}' ${tumor_data}.bai &&
        python3 $__tool_directory__/varscan.py
            --normal '$normal_data'
            --tumor '$tumor_data'
            --normal-purity ${normal_purity}
            --tumor-purity ${tumor_purity}
            #if str($split_output):
                --ofile variants_out
                $split_output
            #else:
                --ofile '$output'
            #end if
            --threads \${GALAXY_SLOTS:-2}
            #if str($call_params.settings) == "custom":
                ## samtools mpileup parameters
                --min-basequal ${call_params.read_selection.min_basequal}
                --min-mapqual ${call_params.read_selection.min_mapqual}
                ${call_params.read_selection.count_orphans}
                ${call_params.read_selection.detect_overlaps}
                --max-pileup-depth ${call_params.read_selection.max_pileup_depth}
                ## VarScan parameters
                --min-coverage ${call_params.min_coverage}
                --min-var-count ${call_params.min_reads2}
                --min-var-freq ${call_params.min_var_freq}
                --min-hom-freq ${call_params.min_freq_for_hom}
                --p-value ${call_params.p_value}
                --somatic-p-value ${call_params.somatic_p_value}
            #end if
            #if str($filter_params.settings) == "no_filter":
                --no-filters
            #else:
                #if str($filter_params.settings) == "dream3_settings":
                    --min-var-count2 3
                    --min-var-count2-lc 1
                    --min-var-count2-depth 10
                    --min-var-freq2 0.05
                    --min-ref-readpos 0.2
                    --min-var-readpos 0.15
                    --min-ref-dist3 0.2
                    --min-var-dist3 0.15
                    --min-ref-len 90
                    --min-var-len 90
                    --max-len-diff 0.05
                    --min-strandedness 0
                    --min-strand-reads 5
                    --min-ref-basequal 15
                    --min-var-basequal 30
                    --max-basequal-diff 50
                    --min-ref-mapqual 20
                    --min-var-mapqual 30
                    --max-mapqual-diff 10
                    --max-ref-mmqs 50
                    --max-var-mmqs 100
                    --min-mmqs-diff 0
                    --max-mmqs-diff 50
                #elif str($filter_params.settings) == "custom":
                    --min-var-count2 ${filter_params.min_var_count}
                    --min-var-count2-lc ${filter_params.min_var_count_lc}
                    --min-var-count2-depth ${filter_params.min_var_count_depth}
                    --min-var-freq2 ${filter_params.min_var_freq2}
                    --min-ref-readpos ${filter_params.min_ref_readpos}
                    --min-var-readpos ${filter_params.min_var_readpos}
                    --min-ref-dist3 ${filter_params.min_ref_dist3}
                    --min-var-dist3 ${filter_params.min_var_dist3}
                    --min-ref-len ${filter_params.min_ref_len}
                    --min-var-len ${filter_params.min_var_len}
                    --max-len-diff ${filter_params.max_len_diff}
                    --min-strandedness ${filter_params.min_strandedness}
                    --min-strand-reads ${filter_params.min_strand_reads}
                    --min-ref-basequal ${filter_params.min_ref_basequal}
                    --min-var-basequal ${filter_params.min_var_basequal}
                    --max-basequal-diff ${filter_params.max_basequal_diff}
                    --min-ref-mapqual ${filter_params.min_ref_mapqual}
                    --min-var-mapqual ${filter_params.min_var_mapqual}
                    --max-mapqual-diff ${filter_params.max_mapqual_diff}
                    --max-ref-mmqs ${filter_params.max_ref_mmqs}
                    --max-var-mmqs ${filter_params.max_var_mmqs}
                    --min-mmqs-diff ${filter_params.min_mmqs_diff}
                    --max-mmqs-diff ${filter_params.max_mmqs_diff}
                #end if
                #if $filter_params.experts_only.compat_opts:
                    #for $opt in str($filter_params.experts_only.compat_opts).split(','):
                        $opt
                    #end for
                #end if
            #end if
            --verbose
            '$ref_genome'