#import re
        #set label = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
        ln -s '$bamfile' one.bam &&
        #if $bamfile.ext == 'bam':
            ln -s '${bamfile.metadata.bam_index}' one.bam.bai &&
        #else:
            ln -s '${bamfile.metadata.cram_index}' one.bam.crai &&
        #end if

        alignmentSieve
        --numberOfProcessors "\${GALAXY_SLOTS:-4}"
        -b one.bam

        --label '$label'

        #if str($filterRNAstrand) != 'no':
            --filterRNAstrand '$filterRNAstrand'
        #end if

        $ignoreDuplicates

        #if $minMappingQuality:
            --minMappingQuality '$minMappingQuality'
        #end if

        #if $samFlagInclude:
            --samFlagInclude $samFlagInclude
        #end if

        #if $samFlagExclude:
            --samFlagExclude $samFlagExclude
        #end if

        #if $minFragmentLength:
            --minFragmentLength $minFragmentLength
        #end if

        #if $maxFragmentLength:
            --maxFragmentLength $maxFragmentLength
        #end if

        #if ' '.join( map(str, $blackListFileName) ) != 'None':
            #set blfiles=[]
            #for $f in $blackListFileName:
                #silent $blfiles.append("'%s'" % $f)
            #end for
            #if $blfiles != ["'None'"]:
                --blackListFileName #echo ' '.join($blfiles)#
            #end if
        #end if

        #if $filterMetrics:
            --filterMetrics '$filterMetricsFile'
        #end if

        #if $filteredOutReads:
            --filteredOutReads '$outFileFiltered'
        #end if

        #if str($shift) != "":
            #set shifts = " ".join(["'{}'".format(x) for x in $shift.split(" ")])
            --shift $shifts
        #elif $ATACshift:
            --ATACshift
        #end if
        #if $BED:
            --BED
            -o '$outFile'
        #elif str($shift) != "" or $ATACshift:
            -o foo.bam &&
            samtools sort -o '$outFile' -T foo.tmp -@ "\${GALAXY_SLOTS:-4}" foo.bam &&
            rm foo.bam
        #else:
            -o '$outFile'
        #end if