#if $refTranscriptSource.TranscriptSource == "history":
            sailfish index
                --transcripts $refTranscriptSource.ownFile
                --kmerSize $refTranscriptSource.kmerSize
                --out ./index_dir
                --threads "\${GALAXY_SLOTS:-4}"
            #set $index_path = './index_dir'
        #else:
            #set $index_path = $refTranscriptSource.index.fields.path
        #end if
        &&
        #set compressed = 'no'
        #if $single_or_paired.single_or_paired_opts == 'single':
            #if $single_or_paired.input_singles.ext == 'fasta':
                #set $ext = 'fasta'
            #else:
                #if $single_or_paired.input_singles.is_of_type("fastq.gz"):
                    #set compressed = 'GZ'
                #else if $single_or_paired.input_singles.is_of_type("fastq.bz2"):
                    #set compressed = 'BZ2'
                #end if
                #set $ext = 'fastq'
            #end if
            ln -s $single_or_paired.input_singles ./single.$ext &&
        #else:
            #if $single_or_paired.input_mate1.ext == 'fasta':
                #set $ext = 'fasta'
            #else:
                #if $single_or_paired.input_mate1.is_of_type("fastq.gz"):
                    #set compressed = 'GZ'
                #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2"):
                    #set compressed = 'BZ2'
                #end if
                #set $ext = 'fastq'
            #end if
            ln -s $single_or_paired.input_mate1 ./mate1.$ext &&
            ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
        #end if
        #if $geneMap:
            ln -s "$geneMap" ./geneMap.$geneMap.ext &&
        #end if
        sailfish quant
            --index $index_path
            #if $single_or_paired.single_or_paired_opts == 'single':
                --libType ${single_or_paired.strandedness}
                #if $compressed == 'GZ':
                    --unmatedReads <(zcat ./single.$ext)
                #else if $compressed == 'BZ2':
                    --unmatedReads <(bzcat ./single.$ext)
                #else:
                    --unmatedReads ./single.$ext
                #end if
            #else:
                #if $compressed == 'GZ':
                    --mates1 <(zcat ./mate1.$ext)
                    --mates2 <(zcat ./mate2.$ext)
                #else if $compressed == 'BZ2':
                    --mates1 <(bzcat ./mate1.$ext)
                    --mates2 <(bzcat ./mate2.$ext)
                #else:
                    --mates1 ./mate1.$ext
                    --mates2 ./mate2.$ext
                #end if
                --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
            #end if
            --output ./results
            $biasCorrect
            $gcBiasCorrect
            --threads "\${GALAXY_SLOTS:-4}"
            $dumpEq
            #if str($gcSizeSamp):
                --gcSizeSamp $gcSizeSamp
            #end if
            #if str($gcSpeedSamp):
                --gcSpeedSamp $gcSpeedSamp
            #end if
            #if str($fldMean):
                --fldMean $fldMean
            #end if
            #if str($fldSD):
                --fldSD $fldSD
            #end if
            #if $maxReadOcc:
                --maxReadOcc $maxReadOcc
            #end if
            #if $geneMap:
                --geneMap ./geneMap.${geneMap.ext}
            #end if
            $strictIntersect
            $noEffectiveLengthCorrection
            $useVBOpt
            $discardOrphans
            $unsmoothedFLD
            --maxFragLen ${maxFragLen}
            --txpAggregationKey '${txpAggregationKey}'
            $ignoreLibCompat
            $enforceLibCompat
            $allowDovetail
            #if str($numBiasSamples):
                --numBiasSamples $numBiasSamples
            #end if
            #if str($numFragSamples):
                --numFragSamples $numFragSamples
            #end if
            #if str($numGibbsSamples):
                --numGibbsSamples $numGibbsSamples
            #end if
            #if str($numBootstraps):
                --numBootstraps $numBootstraps
            #end if