#from os.path import splitext
        #import re
        #def clean_ext($identifier)
            #while $identifier.endswith(('.1', '.fa', '.fq', '.fasta', '.fastq', '.gz', '.gzip', '.sam', '.bam'))
                #set $identifier = splitext($identifier)[0]
            #end while
$identifier#slurp
        #end def
        
    

        mkdir stacks_inputs stacks_outputs

        &&

        #if $sample.is_of_type('fastqsanger')
            #set $data_path = "stacks_inputs/" + $clean_ext($sample.element_identifier) + ".fq"
            #set inputype = "fastq"
        #else if $sample.is_of_type('fastqsanger.gz')
            #set $data_path = "stacks_inputs/" + $clean_ext($sample.element_identifier) + ".fq.gz"
            #set inputype = "gzfastq"
        #else
            #set $data_path = "stacks_inputs/" + $clean_ext($sample.element_identifier) + ".fa"
            #set inputype = "fasta"
        #end if

        ln -s '${sample}' '${data_path}'

        &&

        ustacks

            -p \${GALAXY_SLOTS:-1}

            -f $data_path

            -t $inputype

            ## Batch description
            -i 1

            -m $m
            -M $M
            $R
            $H

            ## Assembly
            $assembly_options.keep_high_cov
            $assembly_options.d
            --max_locus_stacks $assembly_options.max_locus_stacks
            #if str($assembly_options.k_len)
                --k_len $assembly_options.k_len
            #end if

            #if $gapped.use_gapped == "yes"
                --gapped
                --max_gaps $gapped.max_gaps
                --min_aln_len $gapped.min_aln_len
            #end if

            ## snp_model
            #if str( $snp_options.select_model.model_type) == "bounded"
                --model_type bounded
                --bound_low $snp_options.select_model.bound_low
                --bound_high $snp_options.select_model.bound_high
                --alpha $snp_options.select_model.alpha
            #else if str( $snp_options.select_model.model_type) == "snp"
                --model_type snp
                --alpha $snp_options.select_model.alpha
            #else
                --model_type fixed
                --bc_err_freq $bc_err_freq
            #end if

            -o stacks_outputs

            2>&1 | tee ustacks.log

            ## If input is in gz format, stacks will output gzipped files (no option to control this)
            #if $sample.is_of_type('fastqsanger.gz')
                && gunzip stacks_outputs/*.gz
            #end if

            &&

            stacks_summary.py --stacks-prog ustacks --res-dir stacks_outputs --logfile ustacks.log --summary stacks_outputs/summary.html