mkdir ./index
        && mkdir ./output
        #if $refTranscriptSource.TranscriptSource != "indexed":
            && salmon index -i ./index
                --kmerLen '${refTranscriptSource.s_index.kmer}'
                --gencode
                --transcripts '${refTranscriptSource.s_index.fasta}'
            #set $index_path = './index'
        #else
            #set $index_path = $refTranscriptSource.index.fields.path
        #end if
        #if $pairstraight.readselect == 'paired':
            #if $pairstraight.file1.is_of_type("fastq.gz"):
                && cp '${pairstraight.file1}' ./mate1.fastq.gz
                && gunzip ./mate1.fastq.gz
                && cp '${pairstraight.file2}' ./mate2.fastq.gz
                && gunzip ./mate2.fastq.gz
            #else if $pairstraight.file1.is_of_type("fastq.bz2"):
                && cp '${pairstraight.file1}' ./mate1.fastq.bz2
                && bzip2 -d ./mate1.fastq.bz2
                && cp '${pairstraight.file2}' ./mate2.fastq.bz2
                && bzip2 -d ./mate2.fastq.bz2
            #else:
                && ln -s '${pairstraight.file1}' ./mate1.fastq
                && ln -s '${pairstraight.file2}' ./mate2.fastq
            #end if
        #else:
            #if $pairstraight.unmatedreads.is_of_type("fastq.gz"):
                && cp '${pairstraight.unmatedreads}' ./unmate.fastq.gz
                && gunzip ./unmate.fastq.gz
            #else if $pairstraight.unmatedreads.is_of_type("fastq.bz2"):
                && cp '${pairstraight.unmatedreads}' ./unmate.fastq.bz2
                && bzip2 -d unmate.fastq.bz2
            #else:
                && ln -s '${pairstraight.unmatedreads}' ./unmate.fastq
            #end if
        #end if

        && ln -s '${tgmap}' ./alevinmap.tsv
        && salmon alevin -l
        #if $pairstraight.readselect == 'paired':
            #if $pairstraight.libtype.strandedness == 'A'
                A
            #else
                ${pairstraight.libtype.orientation}${pairstraight.libtype.strandedness}
            #end if
            -i $index_path
            -1 ./mate1.fastq
            -2 ./mate2.fastq
        #else:
            '${pairstraight.libtype.strandedness}'
            -i $index_path
            -r zcat ./unmate.fastq
        #end if
        -o ./output
        -p "\${GALAXY_SLOTS:-4}"
        ${protocol_cond.protocol}
        #if $protocol_cond.protocol == '--indropV2'
            --w1 '${protocol_cond.w1}'
        #end if
        --tgMap ./alevinmap.tsv
        #if $whitelist:
            --whitelist '${optional.whitelist}'
        #end if
        #if $optional.numCellBootstraps:
            --numCellBootstraps '${optional.numCellBootstraps}'
        #end if
        #if $optional.forceCells:
            --forceCells '${optional.forceCells}'
        #end if
        #if $optional.expectCells:
            --expectCells '${optional.expectCells}'
        #end if
        #if $optional.mrna:
            --mrna '${optional.mrna}'
        #end if
        #if $optional.rrna:
            --rrna '${optional.rrna}'
        #end if
        #if $optional.keepCBFraction:
            --keepCBFraction '${optional.keepCBFraction}'
        #end if
        ${optional.noDedup}
        #if 'dumpBfh' in $output_files:
            --dumpBfh
        #end if
        #if 'dumpFeatures' in $output_files:
            --dumpFeatures
        #end if
        #if 'dumpUmiGraph' in $output_files:
            --dumpUmiGraph
        #end if
        ${optional.dumpMtx}
        #if $optional.maxNumBarcodes:
            --maxNumBarcodes '${optional.maxNumBarcodes}'
        #end if
        #if $optional.freqThreshold:
            --freqThreshold '${optional.freqThreshold}'
        #end if
        ## && gunzip output/alevin/quants_tier_mat.gz -> the output is binary file
        #if $optional.dumpMtx != "--dumpMtx":
            && python '$__tool_directory__/vpolo_convert.py' -m
        #else:
            && gunzip output/alevin/quants_mat.mtx.gz
        #end if
        #if 'dumpUmiGraph' in $output_files:
            && python '$__tool_directory__/vpolo_convert.py' -u
            && sh '$__tool_directory__/umiout.sh'
        #end if
        ## those gzip file include binary datasets
        ## #if $optional.numCellBootstraps:
        ##    && gunzip output/alevin/quants_mean_mat.gz
        ##    && gunzip output/alevin/quants_var_mat.gz
        ## #end if
        #if 'auxiliar_info' in $output_files
            && tar -zcvf aux_info.tar.gz output/aux_info
        #end if