#if $reference_source.reference_source_selector == 'history':
        ln -f -s '$reference_source.ref_file' reference.fa &&
    #else:
        ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
    #end if
    minimap2
    #if str($fastq_input.analysis_type_selector) == 'self-homology':
        -DP -k19 -w19 -m200
    #elif $fastq_input.analysis_type_selector:
        -x ${fastq_input.analysis_type_selector}
    #end if

    ## indexing options
    $indexing_options.H
    #if str($indexing_options.k):
        -k $indexing_options.k
    #end if
    #if str($indexing_options.w):
        -w $indexing_options.w
    #end if
    #if str($indexing_options.I):
        -I $indexing_options.I
    #end if

    ## Mapping options
    #if str($mapping_options.f):
        -f $mapping_options.f
    #end if
    #if str($mapping_options.min_occ_floor):
        --min-occ-floor $mapping_options.min_occ_floor
    #end if
    --q-occ-frac $mapping_options.q_occ_frac
    #if str($mapping_options.g):
        -g $mapping_options.g
    #end if
    #if str($mapping_options.r):
        -r $mapping_options.r
    #end if
    #if str($mapping_options.n):
        -n $mapping_options.n
    #end if
    #if str($mapping_options.m):
        -m $mapping_options.m
    #end if
    #if str($mapping_options.max_chain_skip):
        --max-chain-skip $mapping_options.max_chain_skip
    #end if
    #if str($mapping_options.max_chain_iter):
        --max-chain-iter $mapping_options.max_chain_iter
    #end if
    $mapping_options.X
    #if str($mapping_options.p):
        -p $mapping_options.p
    #end if
    #if str($mapping_options.N):
        -N $mapping_options.N
    #end if
    #if str($mapping_options.mask_len):
        --mask-len $mapping_options.mask_len
    #end if
    #if str($mapping_options.kmer_ocurrence_interval.interval):
        -U $mapping_options.kmer_ocurrence_interval.lower_limit,$mapping_options.kmer_ocurrence_interval.upper_limit
    #end if
    ## Alignment options
    #if str($alignment_options.splicing.splice_mode) == '--splice':
        --frag=no --splice
        #if str($alignment_options.splicing.G):
            -G $alignment_options.splicing.G
        #end if
        #if str($alignment_options.splicing.C):
            -C $alignment_options.splicing.C
        #end if
        #if $alignment_options.splicing.u:
            -u $alignment_options.splicing.u
        #end if
        $alignment_options.splicing.splice_flank
        #if str($alignment_options.splicing.splice_site_annotations.use_annotations) == 'yes':
            --junc-bed '$alignment_options.splicing.splice_site_annotations.junc_bed'
            --junc-bonus $alignment_options.splicing.splice_site_annotations.junc_bonus
        #end if
    #elif str($mapping_options.F) and 'splice' not in str($fastq_input.analysis_type_selector):
        --frag=yes -F $mapping_options.F
    #end if
    #if str($alignment_options.A):
        -A $alignment_options.A
    #end if
    #if str($alignment_options.B):
        -B $alignment_options.B
    #end if
    #if str($alignment_options.O):
        #if str($alignment_options.O2):
            -O $alignment_options.O,$alignment_options.O2
        #else
            -O $alignment_options.O
        #end if
    #end if
    #if str($alignment_options.E):
        #if str($alignment_options.E2):
            -E $alignment_options.E,$alignment_options.E2
        #else
            -E $alignment_options.E
        #end if
    #end if
    #if str($alignment_options.z):
        #if str($alignment_options.z2):
            -z $alignment_options.z,$alignment_options.z2
        #else
            -z $alignment_options.z
        #end if
    #end if
    #if str($alignment_options.s):
        -s $alignment_options.s
    #end if
    $alignment_options.no_end_flt
    ## Output options
    $io_options.Q
    $io_options.L
    $io_options.c
    #if $io_options.cs:
        --cs=$io_options.cs
    #end if
    $io_options.Y
    #if $io_options.K:
        -K $io_options.K
    #end if
    -t \${GALAXY_SLOTS:-4}
    reference.fa
    #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
        '$fastq_input.fastq_input1'
    #else if $fastq_input.fastq_input_selector == 'paired':
         '$fastq_input.fastq_input1' '$fastq_input.fastq_input2'
    #else if $fastq_input.fastq_input_selector == 'paired_collection':
         '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse'
    #end if
    #if str($io_options.output_format) in ('BAM', 'CRAM'):
        -a | samtools view --no-PG -hT reference.fa
    #end if
    #if $io_options.output_format == 'BAM':
        | samtools sort
        -@\${GALAXY_SLOTS:-2}
        -T "\${TMPDIR:-.}"
        -O $io_options.output_format
        -o '$alignment_output'
    #else if $io_options.output_format == 'CRAM':
        | samtools sort
        -T "\${TMPDIR:-.}"
        -@\${GALAXY_SLOTS:-2}
        -O $io_options.output_format
        $io_options.eqx
        --reference reference.fa
        --output-fmt-option no_ref
        -o '$alignment_output'
    #else:
        > '$alignment_output'
    #end if