mkdir stacks_inputs stacks_outputs

        &&

        #for $input_file in $input_col
            #set $ext = ""
            #if not str($input_file.element_identifier).endswith('.tsv')
                #set $ext = ".tsv"
            #end if
            ln -s '${input_file}' 'stacks_inputs/${input_file.element_identifier}${ext}' &&
        #end for

        rxstacks

            -t \${GALAXY_SLOTS:-1}

            -P stacks_inputs

            ## Batch description
            -b 1

            #if str($options_filtering.lnl)
                --lnl_filter
                --lnl_lim $options_filtering.lnl
            #end if

            $options_filtering.lnl_dist

            #if str($options_filtering.conf)
                --conf_filter
                --conf_lim $options_filtering.conf
            #end if

            #if $options_filtering.prune.prune_haplo == "yes"
                --prune_haplo
                #if str($options_filtering.prune.max_haplo)
                    --max_haplo $options_filtering.prune.max_haplo
                #end if
            #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
            #end if

            -o stacks_outputs