#if str($genome.genome_source) == "history"
    #if $genome.assembly
        #set $genome_assembly = 'genome.fa'
        ln -sf '$genome.assembly' $genome_assembly &&
    #end if
#elif str($genome.genome_source) == "cached"
    #set $genome_assembly = $genome.ref_file.fields.path
#end if
    

#if str($genome_gtf.gtf_source) == "history"
    ln -sf '$genome_gtf.annotation' genome.gtf &&
#end if
    
#set $filter_list = []
#if $options.filters
    #set $filter_list = $options.filters.split(',')
#end if
#if $blacklist
    #if $blacklist.is_of_type('tabular.gz')
        #set $blacklist_file = 'blacklist.tsv.gz'
        ln -sf '$blacklist'  $blacklist_file &&
    #else
        #set $blacklist_file = $blacklist
    #end if
#else
    #if 'blacklist' not in $filter_list
        #silent $filter_list.append('blacklist')
    #end if
#end if
#set $filters = ','.join($filter_list) 
#if $known_fusions
    #if $known_fusions.is_of_type('tabular.gz')
        #set $known_fusions_file = 'known_fusions.tsv.gz'
        ln -sf '$known_fusions'  $known_fusions_file &&
    #else
        #set $known_fusions_file = $known_fusions
    #end if
#end if
#if $tags
    #if $tags.is_of_type('tabular.gz')
        #set $tags_file = 'tags.tsv.gz'
        ln -sf '$tags'  $tags_file &&
    #else
        #set $tags_file = $tags
    #end if
#end if
     arriba 
    -x '$input'
    #if $chimeric
        -c '$chimeric'
    #end if
    -a '$genome_assembly'
    -g 'genome.gtf'
    #if $blacklist
        -b '$blacklist_file'
    #end if
    #if $filters
        -f '$filters'
    #end if
    #if $protein_domains
        -p '$protein_domains'
    #end if
    #if $known_fusions
        -k '$known_fusions_file'
    #end if
    #if $tags
        -t '$tags_file'
    #end if
    #if str($wgs_cond.use_wgs) == "yes"
        -d '$wgs_cond.wgs'
        #if str($wgs_cond.max_genomic_breakpoint_distance)
            -D $wgs_cond.max_genomic_breakpoint_distance
        #end if
    #end if
    -o fusions.tsv
    #if $output_fusions_discarded
    -O fusions.discarded.tsv 
    #end if
    ## Arriba options
    #if $options.gtf_features
        -G '$options.gtf_features'
    #end if
    #if $options.strandedness
        -s $options.strandedness
    #end if
    #if $options.genome_contigs
        -i '$options.genome_contigs'
    #end if
    #if $options.viral_contigs
        -v '$options.viral_contigs'
    #end if
    #if str($options.max_evalue)
        -E $options.max_evalue
    #end if
    #if str($options.min_supporting_reads)
        -S $options.min_supporting_reads
    #end if
    #if str($options.max_mismappers)
        -m $options.max_mismappers
    #end if
    #if str($options.max_homolog_identity)
        -L $options.max_homolog_identity
    #end if
    #if str($options.homopolymer_length)
        -H $options.homopolymer_length
    #end if
    #if str($options.read_through_distance)
        -R $options.read_through_distance
    #end if
    #if str($options.min_anchor_length)
        -A $options.min_anchor_length
    #end if
    #if str($options.many_spliced_events)
        -M $options.many_spliced_events
    #end if
    #if str($options.max_kmer_content)
        -K $options.max_kmer_content
    #end if
    #if str($options.max_mismatch_pvalue)
        -V $options.max_mismatch_pvalue
    #end if
    #if str($options.fragment_length)
        -F $options.fragment_length
    #end if
    #if str($options.max_reads)
        -U $options.max_reads
    #end if
    #if $options.quantile
        -Q $options.quantile
    #end if
    #if str($options.exonic_fraction)
        -e $options.exonic_fraction
    #end if
    #if str($options.top_n)
        -T $options.top_n
    #end if
    #if str($options.covered_fraction)
        -C $options.covered_fraction
    #end if
    #if str($options.max_itd_length)
        -l $options.max_itd_length
    #end if
    #if str($options.min_itd_allele_fraction)
        -z $options.min_itd_allele_fraction
    #end if
    #if str($options.min_itd_supporting_reads)
        -Z $options.min_itd_supporting_reads
    #end if
    $options.duplicate_marking
    $options.fill_discarded_columns
    $options.fill_the_gaps
#if $output_fusion_bams or str($visualization.do_viz) == "yes"
    && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input' > Aligned.sortedByCoord.out.bam
    && samtools index Aligned.sortedByCoord.out.bam
#end if
#if $output_fusions_vcf
    && convert_fusions_to_vcf.sh '$genome_assembly' fusions.tsv fusions.vcf
#end if
#if $output_fusion_bams
    && mkdir fusion_bams 
    && extract_fusion-supporting_alignments.sh fusions.tsv Aligned.sortedByCoord.out.bam 'fusion_bams/fusion'
#end if
#if str($visualization.do_viz) == "yes"
    #set $fusions = 'fusions.tsv'
    && 
draw_fusions.R
    --fusions='$fusions'
    --alignments='Aligned.sortedByCoord.out.bam'
    --annotation='$genome_gtf.annotation'
    --output=fusions.pdf
    #if $visualization.cytobands
    --cytobands='$visualization.cytobands'
    #end if
    #if $protein_domains
    --proteinDomains='$protein_domains'
    #end if
    ## Visualization Options
    #if $visualization.options.transcriptSelection
        --transcriptSelection=$visualization.options.transcriptSelection
    #end if
    #if $visualization.options.minConfidenceForCircosPlot
        --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot
    #end if
    #if $visualization.options.squishIntrons
        --squishIntrons=$visualization.options.squishIntrons
        #if $visualization.options.squishIntrons == 'FALSE' and $visualization.options.showIntergenicVicinity
            --showIntergenicVicinity='$visualization.options.showIntergenicVicinity'
        #end if
    #end if
    #if $visualization.options.mergeDomainsOverlappingBy
        --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy
    #end if
    #if $visualization.options.sampleName
        --sampleName='$visualization.options.sampleName'
    #end if
    #if $visualization.options.printExonLabels
        --printExonLabels=$visualization.options.printExonLabels
    #end if
    #if $visualization.options.coverageRange
        --coverageRange='$visualization.options.coverageRange'
    #end if
    #if $visualization.options.render3dEffect
        --render3dEffect=$visualization.options.render3dEffect
    #end if
    #if $visualization.options.optimizeDomainColors
        --optimizeDomainColors=$visualization.options.optimizeDomainColors
    #end if
    #if $visualization.options.color1
        --color1='$visualization.options.color1'
    #end if
    #if $visualization.options.color2
        --color2='$visualization.options.color2'
    #end if
    #if str($visualization.options.pdfWidth)
        --pdfWidth=$visualization.options.pdfWidth
    #end if
    #if str($visualization.options.pdfHeight)
        --pdfHeight=$visualization.options.pdfHeight
    #end if
    #if $visualization.options.fontFamily
        --fontFamily=$visualization.options.fontFamily
    #end if
    #if str($visualization.options.fontSize)
        --fontSize=$visualization.options.fontSize
    #end if

#end if