#for r in $reuse
    ln -s $r.reuse_file ${r.reuse_step}.gfa &&
#end for

## Preparing files
#set $uncompressed = ('fastqsanger','fastq')
#set $compressed = ('fastqsanger.gz','fastq.gz')
#if str( $paired_unpaired.fastq_input_selector ) == "paired"
    #if $paired_unpaired.fastq_input1.file_ext in $uncompressed
        #set fq1 = "fq1.fastq"
    #elif $paired_unpaired.fastq_input1.file_ext in $compressed
        #set fq1 = "fq1.fastq.gz"
    #end if
    #if $paired_unpaired.fastq_input2.file_ext in $uncompressed
        #set fq2 = "fq2.fastq"
    #elif $paired_unpaired.fastq_input2.file_ext in $compressed
        #set fq2 = "fq2.fastq.gz"
    #end if
    ln -s '${paired_unpaired.fastq_input1}' $fq1 &&
    ln -s '${paired_unpaired.fastq_input2}' $fq2 &&
#elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
    #if $paired_unpaired.fastq_input1.forward.file_ext in $uncompressed
        #set fq1 = "fq1.fastq"
    #elif $paired_unpaired.fastq_input1.forward.file_ext in $compressed
        #set fq1 = "fq1.fastq.gz"
    #end if
    #if $paired_unpaired.fastq_input1.reverse.file_ext in $uncompressed
        #set fq2 = "fq2.fastq"
    #elif $paired_unpaired.fastq_input1.reverse.file_ext in $compressed
        #set fq2 = "fq2.fastq.gz"
    #end if
    ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 &&
    ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 &&
#elif str( $paired_unpaired.fastq_input_selector ) == "single"
    #if $paired_unpaired.fastq_input1.file_ext in $uncompressed
        #set fq = "fq.fastq"
    #elif $paired_unpaired.fastq_input1.file_ext in $compressed
        #set fq = "fq.fastq.gz"
    #end if
    ln -s '${paired_unpaired.fastq_input1}' '$fq' &&
#end if
#if $long
    #if $long.file_ext in $uncompressed
        #set lr = "lr.fastq"
    #elif $long.file_ext in $compressed
        #set lr = "lr.fastq.gz"
    #elif $long.is_of_type('fasta')
        #set lr = "lr.fasta"
    #end if
    ln -s '${long}' '$lr' &&
#end if
## Running Unicycler
unicycler -t "\${GALAXY_SLOTS:-4}"
-o ./
--verbosity 3
#if str( $paired_unpaired.fastq_input_selector ) == "paired"
    -1 '$fq1'
    -2 '$fq2'
#elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
    -1 '$fq1'
    -2 '$fq2'
#elif str( $paired_unpaired.fastq_input_selector ) == "single"
    -s '$fq'
#end if
#if $long
    -l $lr
#end if
## General Unicycler Options section
## ----------------------------------------------------------
--mode '$mode'
--min_fasta_length '$min_fasta_length'
--linear_seqs '$linear_seqs'
#if str($min_anchor_seg_len) != ''
--min_anchor_seg_len '$min_anchor_seg_len'
#end if
## Spades Options section
## ----------------------------------------------------------
--min_kmer_frac '$spades.min_kmer_frac'
--max_kmer_frac '$spades.max_kmer_frac'
#if str($spades.kmers) != ''
--kmers '$spades.kmers'
#end if
--kmer_count '$spades.kmer_count'
--depth_filter '$spades.depth_filter'
#if $spades.largest_component
    --largest_component
#end if
## Rotation Options section
## ----------------------------------------------------------
$rotation.no_rotate
#if $rotation.start_genes
    --start_genes '$rotation.start_genes'
#end if
--start_gene_id '$rotation.start_gene_id'
--start_gene_cov '$rotation.start_gene_cov'
## Graph cleaning Options sdection
## ----------------------------------------------------------
--min_component_size '$graph_clean.min_component_size'
--min_dead_end_size '$graph_clean.min_dead_end_size'
## Long Read Alignment Options
## ----------------------------------------------------------
#if $lr_align.contamination
    --contamination '$lr_align.contamination'
#end if
--scores '${lr_align.scores}'
#if str($lr_align.low_score) != ''
    --low_score '$lr_align.low_score'
#end if
$lr_align.no_simple_bridges
--keep $keep
#if $keep != '0'
    && mkdir 'spades_graphs'
    && mv 00*gfa './spades_graphs/'
#end if
#if $keep == '2' and $long
        && samtools view -@ "\${GALAXY_SLOTS:-4}" -u 'read_alignment/long_read_alignments.sam' | samtools sort -@ "\${GALAXY_SLOTS:-4}" -o 'read_alignment/long_read_alignments.bam'
#end if