#if $select_mode.mode == "paired"
            ln -s '$select_mode.normal' ./normal.bam &&
            ln -s '$select_mode.normal.metadata.bam_index' ./normal.bam.bai &&
        #end if
        ln -s '$select_mode.tumor' ./tumor.bam &&
        ln -s '$select_mode.tumor.metadata.bam_index' ./tumor.bam.bai &&

        ## INDEX REFERENCE FASTA FILE IF FROM HISTORY
        #if $reference_source.reference_source_selector == "history":
            ln -s '$reference_source.ref_file' ./ref.fa &&
            samtools faidx ./ref.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for vardict' >&2 &&
        #else if $reference_source.reference_source_selector == "cached"
            ln -s '$reference_source.ref_file.fields.path' ./ref.fa &&
            ln -s '${reference_source.ref_file.fields.path}.fai' ./ref.fa.fai &&
        #end if

        ## build BED file from chromosome list
        #if $interval_file:
            grep -w -f '$interval_file' ./ref.fa.fai > ./chromosomes.fa.fai &&
        #else
            ln -s ./ref.fa.fai ./chromosomes.fa.fai &&
        #end if
        python '$__tool_directory__/split.py' ./chromosomes.fa.fai "\${VARDICT_CHUNKSIZE:-1000000}" "\${VARDICT_OVERLAP:-150}" > ./regions.bed &&

        vardict-java
        #if $select_mode.mode == "paired"
            -b "./tumor.bam|./normal.bam"
            -N 'Tumor'
        #else
            -b "./tumor.bam"
            -N 'Sample'
        #end if
        -G ./ref.fa
        -z
        -th \${GALAXY_SLOTS:-1}

        -f '$advancedsettings.f'
        -k '$advancedsettings.k'
        -r '$advancedsettings.r'
        -B '$advancedsettings.B'
        -Q '$advancedsettings.Q'
        -q '$advancedsettings.q'
        -m '$advancedsettings.m'
        -T '$advancedsettings.T'
        -X '$advancedsettings.X'
        -P '$advancedsettings.P'
        -o '$advancedsettings.o'
        -O '$advancedsettings.O'
        -V '$advancedsettings.V'

        ## construct VFC table
        -c 1 -S 2 -E 3 -g 4
        ./regions.bed

        ## postprocessing
        #if $select_mode.mode == "paired"
            | testsomatic.R
            | var2vcf_paired.pl
            -N 'Tumor|Normal'
        #else
            | teststrandbias.R
            | var2vcf_valid.pl
            -N 'Sample'
            -E
        #end if
         -f '$advancedsettings.f'

        > '$all_variants' &&

        ## Filter for PASS variants
        awk 'BEGIN {FS=OFS="\t"} substr(\$0, 1, 1) == "#" {print \$0; next} \$7 == "PASS" {print \$0}' '$all_variants' > '$passed_variants'