#if $intervals 
            ln -s '${intervals}' intervals.bed &&
        #end if 
        snpEff -Xmx\${GALAXY_MEMORY_MB:-8192}m eff
        -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
        #if $spliceSiteSize and str($spliceSiteSize) != '':
          -spliceSiteSize "$spliceSiteSize"
        #end if
        #if $spliceRegion.setSpliceRegions == 'yes':
          #if str($spliceRegion.spliceRegionExonSize)
            -spliceRegionExonSize $spliceRegion.spliceRegionExonSize
          #end if
          #if str($spliceRegion.spliceRegionIntronMin)
            -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin
          #end if
          #if str($spliceRegion.spliceRegionIntronMax)
            -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax
          #end if
        #end if
        #if $annotations and str($annotations) != '':
          #echo " "
          #echo ' '.join(str($annotations).split(','))
        #end if
        #if $filterOut and str($filterOut) != '':
          #echo " "
          #echo ' '.join(str($filterOut).split(','))
        #end if
        #if $filter.specificEffects == 'yes' and $filter.effects:
          #for $eff in str($filter.effects).split(','):
            -no $eff
          #end for
        #end if
        #if $transcripts
          -onlyTr '$transcripts'
        #end if
        #if $intervals     ### fix this for multiple dataset input
          -interval intervals.bed
        #end if
        #if $statsFile:
          -stats '$statsFile'
        #end if
        #if $csvStats:
            -csvStats '$csvFile'
        #end if
        #if str($offset) != 'default':
          ${offset}
        #end if
        #if str($chr).strip() != '':
          -chr '$chr'
        #end if
          $noLog
        ## Regulation names can include parentheses: H3K4me3-MSC_(VB)_enriched_sites
        ## Enclose them in in single and double quotes, as the conda snpEff bash script will remove outer quotes
        #if $snpDb.genomeSrc == 'cached':
          -dataDir ${snpDb.genomeVersion.fields.path}
          #if $snpDb.reg_section.regulation and str($snpDb.reg_section.regulation) != '':
            #set $regs = [x for x in str($snpDb.reg_section.regulation).split(',')]
            #for reg in $regs:
              -reg '"${reg}"'
            #end for
          #end if
          $snpDb.genomeVersion
        #elif $snpDb.genomeSrc == 'history':
          -dataDir '${snpDb.snpeff_db.extra_files_path}'
          #if $snpDb.reg_section.regulation and str($snpDb.reg_section.regulation) != '':
            #set $regs = [x for x in str($snpDb.reg_section.regulation).split(',')]
            #for reg in $regs:
              -reg '"${reg}"'
            #end for
          #end if
          '${snpDb.snpeff_db.metadata.genome_version}'
        #elif $snpDb.genomeSrc == 'custom':
            -dataDir '${snpDb.snpeff_db.extra_files_path}'
            -configOption '${snpDb.snpeff_db.metadata.genome_version}'.genome='${snpDb.snpeff_db.metadata.genome_version}'
            -configOption '${snpDb.snpeff_db.metadata.genome_version}'.codonTable='${snpDb.codon_table}'
            '${snpDb.snpeff_db.metadata.genome_version}'
        #else
          -dataDir "\$PWD/temp"
          -download
          '$snpDb.genome_version'
        #end if
        '$input' > '$snpeff_output'
        #if $statsFile:
            &&
            #import os
            #if $csvStats:
                #set $genes_file = str($csvFile) + '.genes.txt'
            #else
                #set $genes_file = str($statsFile) + '.genes.txt'
            #end if
            #set $genes_file_name = os.path.split($genes_file)[-1]
            mkdir '$statsFile.files_path' &&
            mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#'
        #end if
        #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
          &&
          ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
          sed -i.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' '$snpeff_output'
        #end if