#if $input.is_of_type("sam"):
            ## sam input is not supported for paired data
            ## https://github.com/CGATOxford/UMI-tools/issues/483
            ## so convert it to sorted BAM
            ## #set $input_file = $input
            samtools sort --no-PG '$input' -O BAM > 'input.bam' &&
            samtools index -b 'input.bam' &&
            #set $input_file = 'input.bam'
        #else:
            ln -sf '${input}' 'input.bam' &&
            ln -sf '$input.metadata.bam_index' 'input.bam.bai' &&
            #set $input_file = 'input.bam'
        #end if
    

        echo $input.ext &&
        umi_tools dedup
            #if $output_stats_bool
                --output-stats=stats_outputs
            #end if
            
        $gd.buffer_whole_contig
        $gd.whole_contig
        #if $gd.multimapping_detection_method
            --multimapping-detection-method $gd.multimapping_detection_method
        #end if
    
            
        --extract-umi-method $bc.extract_umi_method
        #if str($bc.extract_umi_method) == 'read_id':
            --umi-separator '$bc.umi_separator'
        #else if str($bc.extract_umi_method) == 'tag':
            --umi-tag '$bc.umi_tag'
            #if $bc.umi_tag_split != ''
                --umi-tag-split '$bc.umi_tag_split'
            #end if
            #if $bc.umi_tag_delimiter != ''
                --umi-tag-delimiter '$bc.umi_tag_delimiter'
            #end if
            --cell-tag '$bc.cell_tag'
            #if $bc.cell_tag_split != ''
                --cell-tag-split '$bc.cell_tag_split'
            #end if
            #if $bc.cell_tag_delimiter != ''
                --cell-tag-delimiter '$bc.cell_tag_delimiter'
            #end if
        #end if
    
            
        --method $umi.method
        --edit-distance-threshold $umi.edit_distance_threshold
        $umi.spliced_is_unique
        --soft-clip-threshold $umi.soft_clip_threshold
        $umi.read_length
    
            
        --mapping-quality $sambam.mapping_quality
        --unmapped-reads $sambam.unmapped_reads
        #if $sambam.chimeric_pairs
            --chimeric-pairs $sambam.chimeric_pairs
        #end if
        #if $sambam.unpaired_reads
            --unpaired-reads $sambam.unpaired_reads
        #end if
        $sambam.ignore_umi
        $sambam.ignore_tlen
        #if str($sambam.chrom) != ''
            --chrom '$sambam.chrom'
        #end if
        --subset $sambam.subset
        $sambam.paired
        
        ## see comment in LINK_SAM_BAM_INPUT
        ## #if $input.is_of_type("sam"):
        ##     --in-sam
        ## #end if
    
    
            
            $sc.per_gene
            
            #if str($sc.gene_tag) != "":
                --gene-tag '$sc.gene_tag'
            #end if
            #if str($sc.assigned_status_tag) != "":
                --assigned-status-tag '$sc.assigned_status_tag'
            #end if
            #if str($sc.skip_tags_regex) != "":
                --skip-tags-regex '$sc.skip_tags_regex'
            #end if
            $sc.per_contig
            #if $sc.gene_transcript_map:
                --gene-transcript-map '$sc.gene_transcript_map'
            #end if
            $sc.per_cell
    
    
            
        #if str($advanced.random_seed) != ''
            --random-seed='$advanced.random_seed'
        #end if
    
            -I '$input_file' -S deduped.bam
            ## using samtools sort is a workaround, for the following error that appears when Galaxy
            ## compares the generated file with the one in test-data
            ## `Converting history BAM to SAM failed: 'samtools returned with error 1: stdout=None, stderr=[main_samview] fail to read the header from "/tmp/tmpd8o61jykdedup_out6.bam".\n'. Will compare BAM files`
            ## problem seems to be the BAM file generated with pysam
            ## may be dropped in the future
            --no-sort-output
            
        #if $log:
            --log='$out_log'
        #end if
        --log2stderr
    
            && samtools sort --no-PG deduped.bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' -O BAM