## Link in the input and output files, so Cutadapt can tell their type

#import re
#set read1 = "input_f"
#set read2 = "input_r"
#set paired = False
#set library_type = str($library.type)
#if $library_type == 'paired':
    #set paired = True
    #set input_1 = $library.input_1
    #set input_2 = $library.input_2
    ## Avoid the paired read input files sharing the same name, else the program still runs but 
    ## uses inaccurate results by using only 1 of 2 files.
    #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
    #set read2 = re.sub('[^\w\-\s]', '_', str($library.input_2.element_identifier))
    #if read1 == read2:
        #set read1 = read1 + "_1"
        #set read2 = read2 + "_2"
    #end if
#else if $library_type == 'paired_collection'
    #set paired = True
    #set input_1 = $library.input_1.forward
    #set input_2 = $library.input_1.reverse
    #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.name)) + "_1"
    #set read2 = re.sub('[^\w\-\s]', '_', str($library.input_1.name)) + "_2"
#else
    #set input_1 = $library.input_1
    #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
#end if

#if $input_1.is_of_type("fastq", "fastq.gz", "fastq.bz2"):
    #set ext = ".fq"
#else
    #set ext = ".fa"
#end if
#if $input_1.ext.endswith(".gz"):
    #set ext=ext+".gz"
#elif $input_1.ext.endswith(".bz2")
    #set ext=ext+".bz2"
#end if


#set read1 = $read1 + $ext
#set out1 = "out1" + $ext
#set rest_output = "rest_output" + $ext
#set wild_output = "wild_output" + $ext
#set too_short_output = "too_short_output" + $ext
#set too_long_output = "too_long_output" + $ext
#set untrimmed_output = "untrimmed_output" + $ext
ln -f -s '${input_1}' '$read1' &&

#if $paired:
    #if $input_2.is_of_type("fastq", "fastq.gz", "fastq.bz2"):
        #set ext2 = ".fq"
    #else
        #set ext2 = ".fa"
    #end if
    #if $input_2.ext.endswith(".gz"):
        #set ext2=ext2+".gz"
    #elif $input_2.ext.endswith(".bz2")
        #set ext2=ext2+".bz2"
    #end if
    #set read2 = $read2 + $ext2
    #set out2 = "out2" + $ext2
    #set too_short_paired_output = "too_short_paired_output" + $ext2
    #set too_long_paired_output = "too_long_paired_output" + $ext2
    #set untrimmed_paired_output = "untrimmed_paired_output" + $ext2
    ln -f -s '${input_2}' '$read2' &&
#end if

## Run Cutadapt

#if 'multiple_output' in $output_selector:
    mkdir split &&
#end if

cutadapt

-j=\${GALAXY_SLOTS:-4}

#if 'json_stats' in $output_selector:
    --json stats.json
#end if

#if str( $library.type ) == "single":
    

        ## Read1 trimming

        #set ADAPTER_ARGUMENT="-a"
        #for $a in $library.r1.adapters
            
        #if $a.adapter_source.adapter_source_list == 'builtin':
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else if $a.adapter_source.adapter_source_list == 'file':
            $ADAPTER_ARGUMENT file:'${a.adapter_source.adapter_file}${a.single_noindels}'
        #else if str($a.adapter_source.adapter_name) != "":
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter}${a.single_noindels}'
         #end if
    
        #end for
        
        #set ADAPTER_ARGUMENT="-b"
        #for $a in $library.r1.anywhere_adapters
            
        #if $a.adapter_source.adapter_source_list == 'builtin':
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else if $a.adapter_source.adapter_source_list == 'file':
            $ADAPTER_ARGUMENT file:'${a.adapter_source.adapter_file}${a.single_noindels}'
        #else if str($a.adapter_source.adapter_name) != "":
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter}${a.single_noindels}'
         #end if
    
        #end for
        
        #set ADAPTER_ARGUMENT="-g"
        #for $a in $library.r1.front_adapters
            
        #if $a.adapter_source.adapter_source_list == 'builtin':
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else if $a.adapter_source.adapter_source_list == 'file':
            $ADAPTER_ARGUMENT file:'${a.adapter_source.adapter_file}${a.single_noindels}'
        #else if str($a.adapter_source.adapter_name) != "":
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter}${a.single_noindels}'
         #end if
    
        #end for

        #if str($cut) != '0':
            -u $cut
        #end if

        ## Additional Outputs

        #if 'info_file' in $output_selector:
            --info-file=$info_file
        #end if
        #if 'rest_file' in $output_selector:
            --rest-file='${rest_output}'
        #end if
        #if 'wildcard_file' in $output_selector:
            --wildcard-file='${wild_output}'
        #end if
        #if 'too_short_file' in $output_selector:
            --too-short-output='${too_short_output}'
        #end if
        #if 'too_long_file' in $output_selector:
            --too-long-output='${too_long_output}'
        #end if
        #if 'untrimmed_file' in $output_selector:
            --untrimmed-output='${untrimmed_output}'
        #end if

    
    #if 'multiple_output' in $output_selector:
        --output='split/{name}.${input_1.ext}'
    #else:
        --output='$out1'
    #end if
#else:
    

        ## Read1 trimming

        #set ADAPTER_ARGUMENT="-a"
        #for $a in $library.r1.adapters
            
        #if $a.adapter_source.adapter_source_list == 'builtin':
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else if $a.adapter_source.adapter_source_list == 'file':
            $ADAPTER_ARGUMENT file:'${a.adapter_source.adapter_file}${a.single_noindels}'
        #else if str($a.adapter_source.adapter_name) != "":
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter}${a.single_noindels}'
         #end if
    
        #end for
        
        #set ADAPTER_ARGUMENT="-b"
        #for $a in $library.r1.anywhere_adapters
            
        #if $a.adapter_source.adapter_source_list == 'builtin':
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else if $a.adapter_source.adapter_source_list == 'file':
            $ADAPTER_ARGUMENT file:'${a.adapter_source.adapter_file}${a.single_noindels}'
        #else if str($a.adapter_source.adapter_name) != "":
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter}${a.single_noindels}'
         #end if
    
        #end for
        
        #set ADAPTER_ARGUMENT="-g"
        #for $a in $library.r1.front_adapters
            
        #if $a.adapter_source.adapter_source_list == 'builtin':
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else if $a.adapter_source.adapter_source_list == 'file':
            $ADAPTER_ARGUMENT file:'${a.adapter_source.adapter_file}${a.single_noindels}'
        #else if str($a.adapter_source.adapter_name) != "":
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter}${a.single_noindels}'
         #end if
    
        #end for

        #if str($cut) != '0':
            -u $cut
        #end if

        ## Additional Outputs

        #if 'info_file' in $output_selector:
            --info-file=$info_file
        #end if
        #if 'rest_file' in $output_selector:
            --rest-file='${rest_output}'
        #end if
        #if 'wildcard_file' in $output_selector:
            --wildcard-file='${wild_output}'
        #end if
        #if 'too_short_file' in $output_selector:
            --too-short-output='${too_short_output}'
        #end if
        #if 'too_long_file' in $output_selector:
            --too-long-output='${too_long_output}'
        #end if
        #if 'untrimmed_file' in $output_selector:
            --untrimmed-output='${untrimmed_output}'
        #end if

    
    

        ## Read2 trimming

        #set ADAPTER_ARGUMENT="-A"
        #for $a in $library.r2.adapters2
            
        #if $a.adapter_source.adapter_source_list == 'builtin':
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else if $a.adapter_source.adapter_source_list == 'file':
            $ADAPTER_ARGUMENT file:'${a.adapter_source.adapter_file}${a.single_noindels}'
        #else if str($a.adapter_source.adapter_name) != "":
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter}${a.single_noindels}'
         #end if
    
        #end for
        #set ADAPTER_ARGUMENT="-B"
        #for $a in $library.r2.anywhere_adapters2
            
        #if $a.adapter_source.adapter_source_list == 'builtin':
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else if $a.adapter_source.adapter_source_list == 'file':
            $ADAPTER_ARGUMENT file:'${a.adapter_source.adapter_file}${a.single_noindels}'
        #else if str($a.adapter_source.adapter_name) != "":
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter}${a.single_noindels}'
         #end if
    
        #end for
        #set ADAPTER_ARGUMENT="-G"
        #for $a in $library.r2.front_adapters2
            
        #if $a.adapter_source.adapter_source_list == 'builtin':
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else if $a.adapter_source.adapter_source_list == 'file':
            $ADAPTER_ARGUMENT file:'${a.adapter_source.adapter_file}${a.single_noindels}'
        #else if str($a.adapter_source.adapter_name) != "":
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${a.single_noindels}'
        #else
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter}${a.single_noindels}'
         #end if
    
        #end for

        #if str($library.r2.cut2) != '0':
            -U $library.r2.cut2
        #end if

        ## Additional Outputs - Read 2

        #if 'too_short_file' in $output_selector:
            --too-short-paired-output='${too_short_paired_output}'
        #end if
        #if 'too_long_file' in $output_selector:
            --too-long-paired-output='${too_long_paired_output}'
        #end if
        #if 'untrimmed_file' in $output_selector:
            --untrimmed-paired-output='${untrimmed_paired_output}'
        #end if

    
    --output='$out1'
    --paired-output='$out2'
#end if

--error-rate=$adapter_options.error_rate
--times=$adapter_options.times
--overlap=$adapter_options.overlap
$adapter_options.no_indels
$adapter_options.match_read_wildcards
$adapter_options.no_match_adapter_wildcards
--action=$adapter_options.action
$adapter_options.revcomp

$filter_options.discard_trimmed
$filter_options.discard_untrimmed

#if str($filter_options.minimum_length) and str($library.type) != "single" and str($library.minimum_length2) != '':
    --minimum-length=$filter_options.minimum_length:$library.minimum_length2
#else if str($filter_options.minimum_length):
    --minimum-length=$filter_options.minimum_length
#end if
#if str($filter_options.maximum_length) and str($library.type) != "single" and str($library.maximum_length2) != '':
    --maximum-length=$filter_options.maximum_length:$library.maximum_length2
#else if str($filter_options.maximum_length):
    --maximum-length=$filter_options.maximum_length
#end if
#if str($filter_options.max_n):
    --max-n=$filter_options.max_n
#end if
#if str( $library.type ) != "single":
    #if $filter_options.pair_filter:
        --pair-filter=$filter_options.pair_filter
    #end if
#end if
#if str($filter_options.max_expected_errors):
    --max-expected-errors=$filter_options.max_expected_errors
#end if
$filter_options.discard_cassava

#if $input_1.ext.startswith("fastqillumina") or $input_1.ext.startswith("fastqsolexa")
    --quality-base=64
#end if

#if str($read_mod_options.quality_cutoff) != '0':
   --quality-cutoff=$read_mod_options.quality_cutoff
#end if
#if str($read_mod_options.nextseq_trim) != '0':
    --nextseq-trim=$read_mod_options.nextseq_trim
#end if
$read_mod_options.trim_n
$read_mod_options.poly_a
#if $read_mod_options.strip_suffix != ''
    --strip-suffix $read_mod_options.strip_suffix
#end if
#if str($read_mod_options.shorten_options.shorten_values) == 'True':
    #if str($read_mod_options.shorten_options.shorten_end) == '3prime'
        --length=$read_mod_options.shorten_options.length
    #else
        --length=-$read_mod_options.shorten_options.length
    #end if
#end if
#if str($read_mod_options.length_tag) != '':
    --length-tag='$read_mod_options.length_tag'
#end if
#if str($read_mod_options.rename) != '':
    --rename='$read_mod_options.rename'
#end if
$read_mod_options.zero_cap


'${read1}'
#if $paired:
    '${read2}'
    #if $library.r2.quality_cutoff2:
        -Q=$library.r2.quality_cutoff2
    #end if
#end if

#if 'report' in $output_selector:
    > report.txt
#end if