## Create temporary index for custom reference
    #if str($refGenomeSource.geneSource) == 'history':
        #if $refGenomeSource.genomeFastaFiles.ext == "fasta"
            ln -s '$refGenomeSource.genomeFastaFiles' refgenome.fa &&
        #else
            gunzip -c '$refGenomeSource.genomeFastaFiles' > refgenome.fa &&
        #end if
        mkdir -p tempstargenomedir &&
        STAR
            --runMode genomeGenerate
            --genomeDir 'tempstargenomedir'
            --genomeFastaFiles refgenome.fa
            ## Handle difference between indices with/without annotations
            #if 'GTFconditional' in $refGenomeSource:
                ## GTFconditional exists only in STAR, but not STARsolo
                #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
                    --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
                    --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
                    --sjdbGTFfeatureExon '${refGenomeSource.GTFconditional.sjdbGTFfeatureExon}'
                    #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
                        --sjdbGTFtagExonParentTranscript Parent
                    #end if
                #end if
            #else:
                ## ref genome selection is less complex for STARsolo because
                ## with-gtf is mandatory there
                --sjdbOverhang '${refGenomeSource.sjdbOverhang}'
                --sjdbGTFfile '${refGenomeSource.sjdbGTFfile}'
                --sjdbGTFfeatureExon '${refGenomeSource.sjdbGTFfeatureExon}'
                #if str($refGenomeSource.sjdbGTFfile.ext) == 'gff3':
                    --sjdbGTFtagExonParentTranscript Parent
                #end if
            #end if
            #if str($refGenomeSource.genomeSAindexNbases):
                --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
            #end if
            ## Diploid mode
            #if 'diploidconditional' in $refGenomeSource:
                #if str($refGenomeSource.diploidconditional.diploid) == 'Yes':
                    --genomeTransformVCF '${refGenomeSource.diploidconditional.genomeTransformVCF}'
                    --genomeTransformType Diploid
                #end if   
            #end if
            --runThreadN \${GALAXY_SLOTS:-4}
            ## in bytes
            --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000))
        &&
    #end if
    
    STAR
    
    --runThreadN \${GALAXY_SLOTS:-4}
    --genomeLoad NoSharedMemory
    --genomeDir
    #if str($refGenomeSource.geneSource) == 'history':
        tempstargenomedir
    #else:
        '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
        ## Handle difference between indices with/without annotations
        #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf-with-gtf':
            --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
            --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
            --sjdbGTFfeatureExon '${refGenomeSource.GTFconditional.sjdbGTFfeatureExon}'
            #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
                --sjdbGTFtagExonParentTranscript Parent
            #end if
        #end if
    #end if
    

        --readFilesIn
        #if str($singlePaired.sPaired) == 'paired_collection':
            '$singlePaired.input.forward' '$singlePaired.input.reverse'

            #if $singlePaired.input.forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
                
        --readFilesCommand zcat
    
            #end if
        #else
            '$singlePaired.input1'
            #if str($singlePaired.sPaired) == 'paired':
                '$singlePaired.input2'
            #end if

            #if $singlePaired.input1.is_of_type('fastq.gz', 'fastqsanger.gz'):
                
        --readFilesCommand zcat
    
            #end if
        #end if

        --outSAMtype BAM SortedByCoordinate

        ## Two pass mode
        --twopassMode ${twopass.twopassMode} ${twopass.twopass_read_subset}
        #for $sj_input in $twopass.sj_precalculated:
            '$sj_input'
        #end for
        #if str($twopass.twopassMode) != 'None':
            #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
                ## need to check first if its a cached index or from history
                ## if it's cached then the sjdbGTFfile and sjdbOverhang params are not provided
                #if str($refGenomeSource.geneSource) == 'history':
                    #if not $refGenomeSource.GTFconditional.sjdbGTFfile:
                       ## case of cached index without built-in gene model,
                       ## when user does not supply the optional gtf, but
                       ## specifies the splice junction overhang
                       --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
                    #end if
                #end if
            #end if
        #end if

        --quantMode ${refGenomeSource.GTFconditional.quantmode_output.quantMode}
        #if 'TranscriptomeSAM' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode):
            --quantTranscriptomeBan ${refGenomeSource.GTFconditional.quantmode_output.quantTranscriptomeBan}
        #end if

        ## Output format parameters

        ## Read tags
        #set read_tags = str($oformat.outSAMattributes).split(',')
        #if 'XS' in str($oformat.outSAMattributes):
            ## STAR writes XS tag when --outSAMstrandField intronMotif is used
            $read_tags.remove('XS')
            --outSAMstrandField intronMotif
        #end if
        #if 'HI' in str($oformat.outSAMattributes):
            --outSAMattrIHstart ${oformat.HI_offset}
        #end if
        #set $tag_names = ' '.join($read_tags)
        --outSAMattributes $tag_names

        ## Read FLAG
        --outSAMprimaryFlag ${oformat.outSAMprimaryFlag}

        ## Read MAPQ
        --outSAMmapqUnique ${oformat.outSAMmapqUnique}

        ## Transform diploid mode output to reference coordinates
        #if str($refGenomeSource.geneSource) == 'history':
            #if 'diploidconditional' in $refGenomeSource:
                #if str($refGenomeSource.diploidconditional.diploid) == 'Yes':
                    '${refGenomeSource.diploidconditional.genomeTransformOutput}'
                #end if   
            #end if
        #end if

        ## Output filter parameters

        ## Basic Filters
        #if str($filter.basic_filters) != 'None':
            #set $filter_options = str($filter.basic_filters).split(',')
        #else:
            #set filter_options = []
        #end if
        #if 'exclude_unmapped' in $filter_options:
            $filter_options.remove('exclude_unmapped')
            --outSAMunmapped None
        #else:
            --outSAMunmapped Within
        #end if
        #if '--outFilterIntronMotifs RemoveNoncanonical' in $filter_options:
            ## RemoveNoncanonical excludes a superset of the reads excluded
            ## with RemoveNoncanonicalUnannotated
            #if '--outFilterIntronMotifs RemoveNoncanonicalUnannotated' in $filter_options:
                $filter_options.remove('--outFilterIntronMotifs RemoveNoncanonicalUnannotated')
            #end if
        #end if
        #echo ' '.join($filter_options)

        ## Other Filters
        #if str( $filter.output_params2.output_select2 ) == 'yes':
            --outFilterType $filter.output_params2.outFilterType
            --outFilterMultimapScoreRange $filter.output_params2.outFilterMultimapScoreRange
            --outFilterMultimapNmax $filter.output_params2.outFilterMultimapNmax
            --outFilterMismatchNmax $filter.output_params2.outFilterMismatchNmax
            --outFilterMismatchNoverLmax $filter.output_params2.outFilterMismatchNoverLmax
            --outFilterMismatchNoverReadLmax $filter.output_params2.outFilterMismatchNoverReadLmax
            --outFilterScoreMin $filter.output_params2.outFilterScoreMin
            --outFilterScoreMinOverLread $filter.output_params2.outFilterScoreMinOverLread
            --outFilterMatchNmin $filter.output_params2.outFilterMatchNmin
            --outFilterMatchNminOverLread $filter.output_params2.outFilterMatchNminOverLread
            --outSAMmultNmax $filter.output_params2.outSAMmultNmax
            --outSAMtlen $filter.output_params2.outSAMtlen
        #end if

        ## Other parameters
        #if str( $algo.params.settingsType ) == 'star_fusion':
            ## Preset parameters for STAR-Fusion
            --chimSegmentMin 12
            --chimJunctionOverhangMin 12
            --alignSJDBoverhangMin 10
            --alignMatesGapMax 100000
            --alignIntronMax 100000
            --chimSegmentReadGapMax 3
            --alignSJstitchMismatchNmax 5 -1 5 5
            --peOverlapNbasesMin 12
            --peOverlapMMp 0.1
            --chimMultimapScoreRange 10
            --chimMultimapNmax 10
            --chimNonchimScoreDropMin 10
        
        #elif str( $algo.params.settingsType ) == 'arriba':
            ## Preset parameters for Arriba
            --peOverlapNbasesMin 10
            --alignSplicedMateMapLminOverLmate 0.5
            --alignSJstitchMismatchNmax 5 -1 5 5
            --chimSegmentMin 10
            --chimJunctionOverhangMin 10
            --chimScoreDropMax 30
            --chimScoreJunctionNonGTAG 0
            --chimScoreSeparation 1
            --chimSegmentReadGapMax 3
            --chimMultimapNmax 50

        #elif str( $algo.params.settingsType ) == 'full':
            ## Extended parameter options

            ## Seed parameter options
            --seedSearchStartLmax ${algo.params.seed.seedSearchStartLmax}
            --seedSearchStartLmaxOverLread ${algo.params.seed.seedSearchStartLmaxOverLread}
            --seedSearchLmax ${algo.params.seed.seedSearchLmax}
            --seedMultimapNmax ${algo.params.seed.seedMultimapNmax}
            --seedPerReadNmax ${algo.params.seed.seedPerReadNmax}
            --seedPerWindowNmax ${algo.params.seed.seedPerWindowNmax}
            --seedNoneLociPerWindow ${algo.params.seed.seedNoneLociPerWindow}

            ## Alignment parameter options
            --alignIntronMin ${algo.params.align.alignIntronMin}
            --alignIntronMax ${algo.params.align.alignIntronMax}
            --alignMatesGapMax ${algo.params.align.alignMatesGapMax}
            --alignSJoverhangMin ${algo.params.align.alignSJoverhangMin}
            --alignSJstitchMismatchNmax ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax1} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax2} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax3} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax4}
            --alignSJDBoverhangMin ${algo.params.align.alignSJDBoverhangMin}
            --alignSplicedMateMapLmin ${algo.params.align.alignSplicedMateMapLmin}
            --alignSplicedMateMapLminOverLmate ${algo.params.align.alignSplicedMateMapLminOverLmate}
            --alignWindowsPerReadNmax ${algo.params.align.alignWindowsPerReadNmax}
            --alignTranscriptsPerWindowNmax ${algo.params.align.alignTranscriptsPerWindowNmax}
            --alignTranscriptsPerReadNmax ${algo.params.align.alignTranscriptsPerReadNmax}
            --alignEndsType ${algo.params.align.alignEndsType}
            --peOverlapNbasesMin ${algo.params.align.peOverlapNbasesMin}
            --peOverlapMMp ${algo.params.align.peOverlapMMp}
            ## Chimeric alignment parameter options
            #if str($chimOutType):
                --chimSegmentMin ${algo.params.chim_settings.chimSegmentMin}
                --chimScoreMin ${algo.params.chim_settings.chimScoreMin}
                --chimScoreDropMax $algo.params.chim_settings.chimScoreDropMax
                --chimScoreSeparation $algo.params.chim_settings.chimScoreSeparation
                --chimScoreJunctionNonGTAG $algo.params.chim_settings.chimScoreJunctionNonGTAG
                --chimSegmentReadGapMax $algo.params.chim_settings.chimSegmentReadGapMax
                --chimFilter $algo.params.chim_settings.chimFilter
                --chimJunctionOverhangMin $algo.params.chim_settings.chimJunctionOverhangMin
                --chimMainSegmentMultNmax $algo.params.chim_settings.chimMainSegmentMultNmax
                #if str($chimOutType) == 'Junctions':
                    --chimMultimapNmax $algo.params.chim_settings.chimMultimapNmax
                #else:
                    --chimMultimapNmax 0
                #end if
                --chimMultimapScoreRange $algo.params.chim_settings.chimMultimapScoreRange
            #end if

            ## Limits
                
        --limitOutSJoneRead $getVar('algo.params.junction_limits.limitOutSJoneRead', $getVar('solo.junction_limits.limitOutSJoneRead', 1000))
        --limitOutSJcollapsed $getVar('algo.params.junction_limits.limitOutSJcollapsed', $getVar('solo.junction_limits.limitOutSJcollapsed', 1000000))
        --limitSjdbInsertNsj $getVar('algo.params.junction_limits.limitSjdbInsertNsj', $getVar('solo.junction_limits.limitSjdbInsertNsj', 1000000))
    
        #else:
            ## Go with STAR's default algorithmic settings,
            ## but we need to provide a reasonable default
            ## (taken from STAR-Fusion)
            ## for --chimSegmentMin in case the user enabled chimeric
            ## alignments (the STAR default is 0, which disables chimeric
            ## alignments). For consistency, also set
            ## --chimMultimapNmax to 1 when chimeric alignments are reported
            ## in Junctions format only.
            #if str($chimOutType):
                --chimSegmentMin 12
                #if str($chimOutType) == 'Junctions':
                    --chimMultimapNmax 1
                #end if
            #end if
        #end if

        --outBAMsortingThreadN \${GALAXY_SLOTS:-4}
        --outBAMsortingBinsN $perf.outBAMsortingBinsN
        --winAnchorMultimapNmax $perf.winAnchorMultimapNmax
        --limitBAMsortRAM \$((\${GALAXY_MEMORY_MB:-0}*1000000))

        ## Handle chimeric options and output
        #if str($chimOutType):
            --chimOutType $chimOutType
            #if 'Junctions' in str($chimOutType):
                --chimOutJunctionFormat 1
            #end if
        #end if

        ##outWig:
        
        #if str($outWig.outWigType) != 'None':
            --outWigType '$outWig.outWigType' '$outWig.outWigTypeSecondWord'
            --outWigStrand '$outWig.outWigStrand'
            --outWigReferencesPrefix '$outWig.outWigReferencesPrefix'
            --outWigNorm '$outWig.outWigNorm'
        #end if
    
        &&
        ## recompress BAM output for smaller file size
        samtools view -b -o '$mapped_reads' Aligned.sortedByCoord.out.bam
        #if 'TranscriptomeSAM' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode):
            ## same recompression for optional transcriptome BM
            &&
            samtools view -b -o '$transcriptome_mapped_reads' Aligned.toTranscriptome.out.bam
        #end if
        ##outWig:
        
        #if str($outWig.outWigType) == "bedGraph":
            && mv Signal.Unique.str1.out.bg Signal.Unique.str1.out
            && mv Signal.UniqueMultiple.str1.out.bg Signal.UniqueMultiple.str1.out
            #if str($outWig.outWigStrand) == "Stranded":
                && mv Signal.Unique.str2.out.bg Signal.Unique.str2.out
                && mv Signal.UniqueMultiple.str2.out.bg Signal.UniqueMultiple.str2.out
            #end if
        #elif str($outWig.outWigType) == "wiggle":
            && mv Signal.Unique.str1.out.wig Signal.Unique.str1.out
            && mv Signal.UniqueMultiple.str1.out.wig Signal.UniqueMultiple.str1.out
            #if str($outWig.outWigStrand) == "Stranded":
                && mv Signal.Unique.str2.out.wig Signal.Unique.str2.out
                && mv Signal.UniqueMultiple.str2.out.wig Signal.UniqueMultiple.str2.out
            #end if
        #end if