## salmon uses one thread to much
        ## https://github.com/COMBINE-lab/salmon/issues/993
        SLOTS=\$(( \${GALAXY_SLOTS:-4} > 1 ? \${GALAXY_SLOTS:-4} - 1 : 1 ));

        #set TRANSCRIPTSOURCE_CONDITIONAL = $refTranscriptSource
        
        mkdir ./index &&
        mkdir ./output &&
        #if $TRANSCRIPTSOURCE_CONDITIONAL.TranscriptSource != "indexed":
            #if $TRANSCRIPTSOURCE_CONDITIONAL.s_index.genome
                cat '${TRANSCRIPTSOURCE_CONDITIONAL.s_index.genome}' | grep "^>" | cut -d " " -f 1 > 'decoys.txt' &&
                sed -i.bak -e 's/>//g' 'decoys.txt' &&
                cat '${TRANSCRIPTSOURCE_CONDITIONAL.s_index.fasta}' '${TRANSCRIPTSOURCE_CONDITIONAL.s_index.genome}' > 'input_index.fasta' &&
            #else
                ln -s '${TRANSCRIPTSOURCE_CONDITIONAL.s_index.fasta}' 'input_index.fasta' &&
            #end if
            salmon --no-version-check index -i ./index
                --kmerLen '${TRANSCRIPTSOURCE_CONDITIONAL.s_index.kmer}'
                --gencode
                --threads "\$SLOTS"
                --transcripts 'input_index.fasta'
                #if $TRANSCRIPTSOURCE_CONDITIONAL.s_index.genome
                    --decoy 'decoys.txt'
                #end if
            &&
            #set $index_path = './index'
        #else
            #set $index_path = $TRANSCRIPTSOURCE_CONDITIONAL.index.fields.path
        #end if
        
    

        #if $pairstraight.readselect == 'paired':
            #if $pairstraight.mates.forward.is_of_type("fastq.gz"):
                gunzip -c '${pairstraight.mates.forward}' > ./mate1.fastq &&
                gunzip -c '${pairstraight.mates.reverse}' > ./mate2.fastq &&
            #else if $pairstraight.mates.forward.is_of_type("fastq.bz2"):
                bunzip2 -c '${pairstraight.mates.forward}' > ./mate1.fastq &&
                bunzip2 -c '${pairstraight.mates.reverse}' > ./mate2.fastq &&
            #else:
                ln -s '${pairstraight.mates.forward}' ./mate1.fastq &&
                ln -s '${pairstraight.mates.reverse}' ./mate2.fastq &&
            #end if
        #else:
            #if $pairstraight.unmatedreads.is_of_type("fastq.gz"):
                gunzip -c '${pairstraight.unmatedreads}' > ./unmate.fastq &&
            #else if $pairstraight.unmatedreads.is_of_type("fastq.bz2"):
                bunzip2 -c '${pairstraight.unmatedreads}' > ./unmate.fastq &&
            #else:
                ln -s '${pairstraight.unmatedreads}' ./unmate.fastq &&
            #end if
        #end if

        ln -s '${tgmap}' ./alevinmap.tsv &&
        salmon --no-version-check alevin
        --libType
        #if $pairstraight.readselect == 'paired':
            #if $pairstraight.libtype.strandedness == 'A'
                A
            #else
                ${pairstraight.libtype.orientation}${pairstraight.libtype.strandedness}
            #end if
            --index $index_path
            --mates1 ./mate1.fastq
            --mates2 ./mate2.fastq
        #else:
            '${pairstraight.libtype.strandedness}'
            --index $index_path
            --unmatedReads ./unmate.fastq
        #end if
        -o ./output
        -p "\$SLOTS"
        ${protocol_cond.protocol}
        #if $protocol_cond.protocol == '--indropV2'
            --w1 '${protocol_cond.w1}'
        #end if
        --tgMap ./alevinmap.tsv
        #if $whitelist:
            --whitelist '${optional.whitelist}'
        #end if
        --numCellBootstraps '${optional.numCellBootstraps}'
        --forceCells '${optional.forceCells}'
        --expectCells '${optional.expectCells}'
        #if $optional.mrna:
            --mrna '${optional.mrna}'
        #end if
        #if $optional.rrna:
            --rrna '${optional.rrna}'
        #end if
        --minScoreFraction '${optional.minScoreFraction}'
        --keepCBFraction '${optional.keepCBFraction}'
        ${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
        ${optional.dumpMtx}
        --maxNumBarcodes '${optional.maxNumBarcodes}'
        --freqThreshold '${optional.freqThreshold}'
        ## && 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
            && bash '$__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