#if $input_type.options_type_selector == "single"

            #if $input_type.input_single.is_of_type('fastqsanger')
                #set $ext = ".fq"
                #set inputype = "fastq"
            #else
                #set $ext = ".fq.gz"
                #set inputype = "gzfastq"
            #end if

            ln -s '$input_type.input_single' R1$ext &&
        #else

            #if $input_type.inputs_paired1.is_of_type('fastqsanger')
                #set $ext = ".fq"
                #set inputype = "fastq"
            #else
                #set $ext = ".fq.gz"
                #set inputype = "gzfastq"
            #end if

            ln -s '$input_type.inputs_paired1' R1$ext &&
            ln -s '$input_type.inputs_paired2' R2$ext &&
        #end if

        mkdir stacks_outputs

        &&

        process_radtags

            #if $input_type.options_type_selector == "single"
                -f R1$ext
            #else
                -1 R1$ext
                -2 R2$ext
            #end if

            -i $inputype
            -b '$barcode'

            $input_type.barcode_encoding

            #if str( $options_enzyme.options_enzyme_selector ) == "1"
                -e $options_enzyme.enzyme
            #else
                --renz_1 $options_enzyme.enzyme --renz_2 $options_enzyme.enzyme2
            #end if

            #if str( $outype ) != "auto"
                -y $outype
            #end if

            $capture

            $options_advanced.retain_header

            #if str($options_advanced.truncate)
                -t $options_advanced.truncate
            #end if

            -w $options_advanced.sliding

            $options_advanced.remove

            $options_advanced.discard
            -s $options_advanced.score

            $options_advanced.rescue

            -o stacks_outputs