R/prepare_params.R

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

#' @title Prepare params
#'
#' @description This function prepares main parameters
#'
#' @include create_dir.R
#' @include export_params.R
#' @include load_yaml_files.R
#'
#' @param params_small params_small
#' @param params_advanced params_advanced
#' @param step Step
#'
#' @return NULL
#'
#' @export
#'
#' @examples NULL
prepare_params <- function(params_small = get_params(step = "prepare_params"),
                           params_advanced = get_params(step = "prepare_params_advanced"),
                           step = NA) {
  list <- load_yaml_files()
  yamls_params <- list$yamls_params

  log_debug(x = "All params")
  ann_can_fin <- params_advanced$annotations$candidates$final
  ann_ms1only <- params_advanced$annotations$ms1only
  ann_ms2_app <- params_advanced$annotations$ms2approx
  ann_thr_con <- params_advanced$annotations$thresholds$consistency
  ann_thr_ms1_bio <- params_advanced$annotations$thresholds$ms1$biological
  ann_thr_ms1_che <- params_advanced$annotations$thresholds$ms1$chemical
  ann_thr_ms1_con <- params_advanced$annotations$thresholds$ms1$condition
  ann_thr_ms2_sim_ann <- params_advanced$annotations$thresholds$ms2$similarity$annotation
  ann_thr_ms2_sim_edg <- params_advanced$annotations$thresholds$ms2$similarity$edges
  fil_pat <- params_advanced$files$pattern
  fil_ann_raw_spe <- params_advanced$files$annotations$raw$spectral
  fil_ann_raw_spe_gnp <- params_advanced$files$annotations$raw$spectral$gnps
  fil_ann_raw_spe_sir <- params_advanced$files$annotations$raw$spectral$sirius
  fil_ann_raw_spe_spe <- params_advanced$files$annotations$raw$spectral$spectral
  fil_ann_raw_sir <- params_advanced$files$annotations$raw$sirius
  fil_ann_pre_can <- params_advanced$files$annotations$prepared$canopus
  fil_ann_pre_for <- params_advanced$files$annotations$prepared$formula
  fil_ann_pre_str <- params_advanced$files$annotations$prepared$structural
  fil_ann_pre_str_gnp <- params_advanced$files$annotations$prepared$structural$gnps
  fil_ann_pre_str_ms1 <- params_advanced$files$annotations$prepared$structural$ms1
  fil_ann_pre_str_sir <- params_advanced$files$annotations$prepared$structural$sirius
  fil_ann_pre_str_spe <- params_advanced$files$annotations$prepared$structural$spectral
  fil_ann_fil <- params_advanced$files$annotations$filtered
  fil_ann_pro <- params_advanced$files$annotations$processed
  fil_fea_raw <- params_advanced$files$features$raw
  fil_fea_pre <- params_advanced$files$features$prepared
  fil_lib_sop_raw_clo <- params_advanced$files$libraries$sop$raw$closed
  fil_lib_sop_raw_ecm <- params_advanced$files$libraries$sop$raw$ecmdb
  fil_lib_sop_raw_hmd <- params_advanced$files$libraries$sop$raw$hmdb
  fil_lib_sop_raw_lot <- params_advanced$files$libraries$sop$raw$lotus
  fil_lib_sop_pre <- params_advanced$files$libraries$sop$prepared
  fil_lib_sop_pre_clo <- params_advanced$files$libraries$sop$prepared$closed
  fil_lib_sop_pre_ecm <- params_advanced$files$libraries$sop$prepared$ecmdb
  fil_lib_sop_pre_hmd <- params_advanced$files$libraries$sop$prepared$hmdb
  fil_lib_sop_pre_lot <- params_advanced$files$libraries$sop$prepared$lotus
  fil_lib_sop_pre_rt <- params_advanced$files$libraries$sop$prepared$rt
  fil_lib_sop_mer_key <- params_advanced$files$libraries$sop$merged$keys
  fil_lib_sop_mer_org_nam <- params_advanced$files$libraries$sop$merged$organisms$names
  fil_lib_sop_mer_org_tax_ott <- params_advanced$files$libraries$sop$merged$organisms$taxonomies$ott
  fil_lib_sop_mer_str_ste <- params_advanced$files$libraries$sop$merged$structures$stereo
  fil_lib_sop_mer_str_met <- params_advanced$files$libraries$sop$merged$structures$metadata
  fil_lib_sop_mer_str_nam <- params_advanced$files$libraries$sop$merged$structures$names
  fil_lib_sop_mer_str_tax_cla <- params_advanced$files$libraries$sop$merged$structures$taxonomies$cla
  fil_lib_sop_mer_str_tax_npc <- params_advanced$files$libraries$sop$merged$structures$taxonomies$npc
  fil_lib_spe_exp_neg <- params_advanced$files$libraries$spectral$exp$neg
  fil_lib_spe_exp_pos <- params_advanced$files$libraries$spectral$exp$pos
  fil_lib_spe_exp_raw <- params_advanced$files$libraries$spectral$exp$raw
  fil_lib_spe_is_neg <- params_advanced$files$libraries$spectral$is$neg
  fil_lib_spe_is_pos <- params_advanced$files$libraries$spectral$is$pos
  fil_lib_spe_is_raw <- params_advanced$files$libraries$spectral$is$raw
  fil_lib_tem_exp_csv <- params_advanced$files$libraries$temporal$exp$csv
  fil_lib_tem_exp_mgf_neg <- params_advanced$files$libraries$temporal$exp$mgf$neg
  fil_lib_tem_exp_mgf_pos <- params_advanced$files$libraries$temporal$exp$mgf$pos
  fil_lib_tem_is_csv <- params_advanced$files$libraries$temporal$is$csv
  fil_lib_tem_is_mgf_neg <- params_advanced$files$libraries$temporal$is$mgf$neg
  fil_lib_tem_is_mgf_pos <- params_advanced$files$libraries$temporal$is$mgf$pos
  fil_lib_tem_pre <- params_advanced$files$libraries$temporal$prepared
  fil_net_spe_edg_raw <- params_advanced$files$networks$spectral$edges$raw
  fil_net_spe_edg_raw_ms1 <- params_advanced$files$networks$spectral$edges$raw$ms1
  fil_net_spe_edg_raw_spe <- params_advanced$files$networks$spectral$edges$raw$spectral
  fil_net_spe_edg_pre <- params_advanced$files$networks$spectral$edges$prepared
  fil_net_spe_com_raw <- params_advanced$files$networks$spectral$components$raw
  fil_net_spe_com_pre <- params_advanced$files$networks$spectral$components$prepared
  fil_met_raw <- params_advanced$files$metadata$raw
  fil_met_pre <- params_advanced$files$metadata$prepared
  fil_spe_raw <- params_advanced$files$spectral$raw
  gnps_id <- params_advanced$gnps$id
  gnps_workflow <- params_advanced$gnps$workflow
  ms_add_neg <- params_advanced$ms$adducts$neg
  ms_add_pos <- params_advanced$ms$adducts$pos
  ms_clu_neg <- params_advanced$ms$clusters$neg
  ms_clu_pos <- params_advanced$ms$clusters$pos
  ms_neu <- params_advanced$ms$neutral_losses
  ms_pol <- params_advanced$ms$polarity
  ms_thr_ms2_int <- params_advanced$ms$thresholds$ms2$intensity
  ms_tol_mas_ppm_ms1 <- params_advanced$ms$tolerances$mass$ppm$ms1
  ms_tol_mas_ppm_ms2 <- params_advanced$ms$tolerances$mass$ppm$ms2
  ms_tol_mas_dal_ms1 <- params_advanced$ms$tolerances$mass$dalton$ms1
  ms_tol_mas_dal_ms2 <- params_advanced$ms$tolerances$mass$dalton$ms2
  ms_tol_rt_min <- params_advanced$ms$tolerances$rt$minutes
  names_extension <- params_advanced$names$extension
  names_features <- params_advanced$names$features
  names_filename <- params_advanced$names$filename
  names_inchikey <- params_advanced$names$inchikey
  names_mgf_ad <- params_advanced$names$mgf$adduct
  names_mgf_ce <- params_advanced$names$mgf$collision_energy
  names_mgf_ci <- params_advanced$names$mgf$compound_id
  names_mgf_em <- params_advanced$names$mgf$exact_mass
  names_mgf_in <- params_advanced$names$mgf$inchi
  names_mgf_io <- params_advanced$names$mgf$inchi_no_stereo
  names_mgf_ik <- params_advanced$names$mgf$inchikey
  names_mgf_il <- params_advanced$names$mgf$inchikey_no_stereo
  names_mgf_mf <- params_advanced$names$mgf$molecular_formula
  names_mgf_na <- params_advanced$names$mgf$name
  names_mgf_po <- params_advanced$names$mgf$polarity
  names_mgf_rt <- params_advanced$names$mgf$retention_time
  names_mgf_sm <- params_advanced$names$mgf$smiles
  names_mgf_sn <- params_advanced$names$mgf$smiles_no_stereo
  names_mgf_si <- params_advanced$names$mgf$spectrum_id
  names_mgf_sp <- params_advanced$names$mgf$splash
  names_mgf_sy <- params_advanced$names$mgf$synonyms
  names_mgf_xl <- params_advanced$names$mgf$xlogp
  names_precursor <- params_advanced$names$precursor
  names_rt_fea <- params_advanced$names$rt$features
  names_rt_lib <- params_advanced$names$rt$library
  names_smiles <- params_advanced$names$smiles
  names_source <- params_advanced$names$source
  names_target <- params_advanced$names$target
  names_taxon <- params_advanced$names$taxon
  org_can <- params_advanced$organisms$candidates
  org_fil_mod <- params_advanced$organisms$filter$mode
  org_fil_lev <- params_advanced$organisms$filter$level
  org_fil_val <- params_advanced$organisms$filter$value
  org_tax <- params_advanced$organisms$taxon
  too_met <- params_advanced$tools$metadata
  too_net_spe_com <- params_advanced$tools$networks$spectral$components
  too_net_spe_edg <- params_advanced$tools$networks$spectral$edges
  too_sir_ver <- params_advanced$tools$sirius$version
  too_tax_bio <- params_advanced$tools$taxonomies$biological
  too_tax_che <- params_advanced$tools$taxonomies$chemical
  units_rt <- params_advanced$units$rt
  wei_glo_bio <- params_advanced$weights$global$biological
  wei_glo_che <- params_advanced$weights$global$chemical
  wei_glo_spe <- params_advanced$weights$global$spectral
  wei_bio_01 <- params_advanced$weights$biological$domain
  wei_bio_02 <- params_advanced$weights$biological$kingdom
  wei_bio_03 <- params_advanced$weights$biological$phylum
  wei_bio_04 <- params_advanced$weights$biological$class
  wei_bio_05 <- params_advanced$weights$biological$order
  wei_bio_06 <- params_advanced$weights$biological$infraorder
  wei_bio_07 <- params_advanced$weights$biological$family
  wei_bio_08 <- params_advanced$weights$biological$subfamily
  wei_bio_09 <- params_advanced$weights$biological$tribe
  wei_bio_10 <- params_advanced$weights$biological$subtribe
  wei_bio_11 <- params_advanced$weights$biological$genus
  wei_bio_12 <- params_advanced$weights$biological$subgenus
  wei_bio_13 <- params_advanced$weights$biological$species
  wei_bio_14 <- params_advanced$weights$biological$subspecies
  wei_bio_15 <- params_advanced$weights$biological$variety
  wei_che_11 <- params_advanced$weights$chemical$cla$kingdom
  wei_che_21 <- params_advanced$weights$chemical$npc$pathway
  wei_che_12 <- params_advanced$weights$chemical$cla$superclass
  wei_che_22 <- params_advanced$weights$chemical$npc$superclass
  wei_che_13 <- params_advanced$weights$chemical$cla$class
  wei_che_23 <- params_advanced$weights$chemical$npc$class
  wei_che_14 <- params_advanced$weights$chemical$cla$parent
  opt_cpd_nam <- params_advanced$options$compounds_names
  opt_for <- params_advanced$options$force
  opt_rem_tie <- params_advanced$options$remove_ties
  opt_sum <- params_advanced$options$summarise

  log_debug(x = "Small params")
  fil_pat <- params_small$files$pattern
  fil_fea_raw <- params_small$files$features$raw
  fil_met_raw <- params_small$files$metadata$raw
  fil_spe_raw <- params_small$files$spectral$raw
  fil_ann_raw_spe_sir <- params_small$files$annotations$raw$spectral$sirius
  ms_pol <- params_small$ms$polarity
  org_tax <- params_small$organisms$taxon
  opt_sum <- params_small$options$summarise

  if (!is.null(org_tax)) {
    if (org_tax == "") {
      org_tax <- NULL
    } else {
      fil_met_raw <- NULL
    }
  }

  log_debug(x = "Changing params")
  switch(step,
    annotate_masses = {
      yamls_params$annotate_masses$files$annotations$prepared$structural <-
        fil_ann_pre_str
      yamls_params$annotate_masses$files$features$prepared <-
        fil_fea_pre
      yamls_params$annotate_masses$files$libraries$sop$merged$keys <-
        fil_lib_sop_mer_key
      yamls_params$annotate_masses$files$libraries$sop$merged$structures$stereo <-
        fil_lib_sop_mer_str_ste
      yamls_params$annotate_masses$files$libraries$sop$merged$structures$metadata <-
        fil_lib_sop_mer_str_met
      yamls_params$annotate_masses$files$libraries$sop$merged$structures$names <-
        fil_lib_sop_mer_str_nam
      yamls_params$annotate_masses$files$libraries$sop$merged$structures$taxonomies$cla <-
        fil_lib_sop_mer_str_tax_cla
      yamls_params$annotate_masses$files$libraries$sop$merged$structures$taxonomies$npc <-
        fil_lib_sop_mer_str_tax_npc
      yamls_params$annotate_masses$files$networks$spectral$edges$raw$ms1 <-
        fil_net_spe_edg_raw_ms1
      yamls_params$annotate_masses$ms$adducts$neg <-
        ms_add_neg
      yamls_params$annotate_masses$ms$adducts$pos <-
        ms_add_pos
      yamls_params$annotate_masses$ms$clusters$neg <-
        ms_clu_neg
      yamls_params$annotate_masses$ms$clusters$pos <-
        ms_clu_pos
      yamls_params$annotate_masses$ms$neutral_losses <-
        ms_neu
      yamls_params$annotate_masses$ms$polarity <-
        ms_pol
      yamls_params$annotate_masses$ms$tolerances$mass$ppm$ms1 <-
        ms_tol_mas_ppm_ms1
      yamls_params$annotate_masses$ms$tolerances$mass$dalton$ms1 <-
        ms_tol_mas_dal_ms1
      yamls_params$annotate_masses$ms$tolerances$rt$minutes <-
        ms_tol_rt_min
      yamls_params$annotate_masses$names$source <-
        names_source
      yamls_params$annotate_masses$names$target <-
        names_target
      yamls_params$annotate_masses$options$force <-
        opt_for
    },
    annotate_spectra = {
      yamls_params$annotate_spectra$annotations$ms2approx <-
        ann_ms2_app
      yamls_params$annotate_spectra$annotations$thresholds$ms2$similarity$annotation <-
        ann_thr_ms2_sim_ann
      yamls_params$annotate_spectra$files$annotations$raw$spectral$spectral <-
        fil_ann_raw_spe_spe
      yamls_params$annotate_spectra$files$libraries$spectral$exp$neg <-
        fil_lib_spe_exp_neg
      yamls_params$annotate_spectra$files$libraries$spectral$exp$pos <-
        fil_lib_spe_exp_pos
      yamls_params$annotate_spectra$files$libraries$spectral$is$neg <-
        fil_lib_spe_is_neg
      yamls_params$annotate_spectra$files$libraries$spectral$is$pos <-
        fil_lib_spe_is_pos
      yamls_params$annotate_spectra$files$spectral$raw <-
        fil_spe_raw
      yamls_params$annotate_spectra$ms$thresholds$ms2$intensity <-
        ms_thr_ms2_int
      yamls_params$annotate_spectra$ms$polarity <-
        ms_pol
      yamls_params$annotate_spectra$ms$tolerances$mass$ppm$ms2 <-
        ms_tol_mas_ppm_ms2
      yamls_params$annotate_spectra$ms$tolerances$mass$dalton$ms2 <-
        ms_tol_mas_dal_ms2
    },
    create_components = {
      yamls_params$create_components$files$networks$spectral$edges$prepared <-
        fil_net_spe_edg_pre
      yamls_params$create_components$files$networks$spectral$components$raw <-
        fil_net_spe_com_raw
    },
    create_edges_spectra = {
      yamls_params$create_edges_spectra$annotations$thresholds$ms2$similarity$edges <-
        ann_thr_ms2_sim_edg
      yamls_params$create_edges_spectra$files$networks$spectral$edges$raw$spectral <-
        fil_net_spe_edg_raw_spe
      yamls_params$create_edges_spectra$files$spectral$raw <-
        fil_spe_raw
      yamls_params$create_edges_spectra$ms$thresholds$ms2$intensity <-
        ms_thr_ms2_int
      yamls_params$create_edges_spectra$ms$tolerances$mass$ppm$ms2 <-
        ms_tol_mas_ppm_ms2
      yamls_params$create_edges_spectra$ms$tolerances$mass$dalton$ms2 <-
        ms_tol_mas_dal_ms2
      yamls_params$create_edges_spectra$names$source <-
        names_source
      yamls_params$create_edges_spectra$names$target <-
        names_target
    },
    filter_annotations = {
      yamls_params$filter_annotations$files$annotations$filtered <-
        fil_ann_fil
      yamls_params$filter_annotations$files$annotations$prepared$structural <-
        fil_ann_pre_str
      yamls_params$filter_annotations$files$features$prepared <-
        fil_fea_pre
      yamls_params$filter_annotations$files$libraries$temporal$prepared <-
        fil_lib_tem_pre
      yamls_params$filter_annotations$ms$tolerances$rt$minutes <-
        ms_tol_rt_min
    },
    prepare_annotations_gnps = {
      yamls_params$prepare_annotations_gnps$files$annotations$raw$spectral$gnps <-
        fil_ann_raw_spe_gnp
      yamls_params$prepare_annotations_gnps$files$annotations$prepared$structural$gnps <-
        fil_ann_pre_str_gnp
      yamls_params$prepare_annotations_gnps$files$libraries$sop$merged$structures$stereo <-
        fil_lib_sop_mer_str_ste
      yamls_params$prepare_annotations_gnps$files$libraries$sop$merged$structures$metadata <-
        fil_lib_sop_mer_str_met
      yamls_params$prepare_annotations_gnps$files$libraries$sop$merged$structures$names <-
        fil_lib_sop_mer_str_nam
      yamls_params$prepare_annotations_gnps$files$libraries$sop$merged$structures$taxonomies$cla <-
        fil_lib_sop_mer_str_tax_cla
      yamls_params$prepare_annotations_gnps$files$libraries$sop$merged$structures$taxonomies$npc <-
        fil_lib_sop_mer_str_tax_npc
    },
    prepare_annotations_sirius = {
      yamls_params$prepare_annotations_sirius$files$annotations$raw$sirius <-
        fil_ann_raw_sir
      yamls_params$prepare_annotations_sirius$files$annotations$prepared$canopus <-
        fil_ann_pre_can
      yamls_params$prepare_annotations_sirius$files$annotations$prepared$formula <-
        fil_ann_pre_for
      yamls_params$prepare_annotations_sirius$files$annotations$prepared$structural$sirius <-
        fil_ann_pre_str_sir
      yamls_params$prepare_annotations_sirius$files$libraries$sop$merged$structures$stereo <-
        fil_lib_sop_mer_str_ste
      yamls_params$prepare_annotations_sirius$files$libraries$sop$merged$structures$metadata <-
        fil_lib_sop_mer_str_met
      yamls_params$prepare_annotations_sirius$files$libraries$sop$merged$structures$names <-
        fil_lib_sop_mer_str_nam
      yamls_params$prepare_annotations_sirius$files$libraries$sop$merged$structures$taxonomies$cla <-
        fil_lib_sop_mer_str_tax_cla
      yamls_params$prepare_annotations_sirius$files$libraries$sop$merged$structures$taxonomies$npc <-
        fil_lib_sop_mer_str_tax_npc
      yamls_params$prepare_annotations_sirius$tools$sirius$version <-
        too_sir_ver
    },
    prepare_annotations_spectra = {
      yamls_params$prepare_annotations_spectra$files$annotations$raw$spectral$spectral <-
        fil_ann_raw_spe_spe
      yamls_params$prepare_annotations_spectra$files$annotations$prepared$structural$spectral <-
        fil_ann_pre_str_spe
      yamls_params$prepare_annotations_spectra$files$libraries$sop$merged$structures$stereo <-
        fil_lib_sop_mer_str_ste
      yamls_params$prepare_annotations_spectra$files$libraries$sop$merged$structures$metadata <-
        fil_lib_sop_mer_str_met
      yamls_params$prepare_annotations_spectra$files$libraries$sop$merged$structures$names <-
        fil_lib_sop_mer_str_nam
      yamls_params$prepare_annotations_spectra$files$libraries$sop$merged$structures$taxonomies$cla <-
        fil_lib_sop_mer_str_tax_cla
      yamls_params$prepare_annotations_spectra$files$libraries$sop$merged$structures$taxonomies$npc <-
        fil_lib_sop_mer_str_tax_npc
    },
    prepare_features_components = {
      yamls_params$prepare_features_components$files$networks$spectral$components$raw <-
        fil_net_spe_com_raw
      yamls_params$prepare_features_components$files$networks$spectral$components$prepared <-
        fil_net_spe_com_pre
    },
    prepare_features_edges = {
      yamls_params$prepare_features_edges$files$networks$spectral$edges$raw$ms1 <-
        fil_net_spe_edg_raw_ms1
      yamls_params$prepare_features_edges$files$networks$spectral$edges$raw$spectral <-
        fil_net_spe_edg_raw_spe
      yamls_params$prepare_features_edges$files$networks$spectral$edges$prepared <-
        fil_net_spe_edg_pre
      yamls_params$prepare_features_edges$names$source <-
        names_source
      yamls_params$prepare_features_edges$names$target <-
        names_target
    },
    prepare_features_tables = {
      yamls_params$prepare_features_tables$files$features$raw <-
        fil_fea_raw
      yamls_params$prepare_features_tables$files$features$prepared <-
        fil_fea_pre
      yamls_params$prepare_features_tables$names$features <-
        names_features
      yamls_params$prepare_features_tables$names$precursor <-
        names_precursor
      yamls_params$prepare_features_tables$names$rt$features <-
        names_rt_fea
    },
    prepare_libraries_rt = {
      yamls_params$prepare_libraries_rt$files$libraries$sop$prepared$rt <-
        fil_lib_sop_pre_rt
      yamls_params$prepare_libraries_rt$files$libraries$temporal$exp$csv <-
        fil_lib_tem_exp_csv
      yamls_params$prepare_libraries_rt$files$libraries$temporal$exp$mgf$neg <-
        fil_lib_tem_exp_mgf_neg
      yamls_params$prepare_libraries_rt$files$libraries$temporal$exp$mgf$pos <-
        fil_lib_tem_exp_mgf_pos
      yamls_params$prepare_libraries_rt$files$libraries$temporal$is$csv <-
        fil_lib_tem_is_csv
      yamls_params$prepare_libraries_rt$files$libraries$temporal$is$mgf$neg <-
        fil_lib_tem_is_mgf_neg
      yamls_params$prepare_libraries_rt$files$libraries$temporal$is$mgf$pos <-
        fil_lib_tem_is_mgf_pos
      yamls_params$prepare_libraries_rt$files$libraries$temporal$prepared <-
        fil_lib_tem_pre
      yamls_params$prepare_libraries_rt$names$inchikey <-
        names_inchikey
      yamls_params$prepare_libraries_rt$names$mgf$inchikey <-
        names_mgf_ik
      yamls_params$prepare_libraries_rt$names$mgf$retention_time <-
        names_mgf_rt
      yamls_params$prepare_libraries_rt$names$mgf$smiles <-
        names_mgf_sm
      yamls_params$prepare_libraries_rt$names$rt$library <-
        names_rt_lib
      yamls_params$prepare_libraries_rt$names$smiles <-
        names_smiles
      yamls_params$prepare_libraries_rt$units$rt <-
        units_rt
    },
    prepare_libraries_sop_closed = {
      yamls_params$prepare_libraries_sop_closed$files$libraries$sop$raw$closed <-
        fil_lib_sop_raw_clo
      yamls_params$prepare_libraries_sop_closed$files$libraries$sop$prepared$closed <-
        fil_lib_sop_pre_clo
    },
    prepare_libraries_sop_ecmdb = {
      yamls_params$prepare_libraries_sop_ecmdb$files$libraries$sop$raw$ecmdb <-
        fil_lib_sop_raw_ecm
      yamls_params$prepare_libraries_sop_ecmdb$files$libraries$sop$prepared$ecmdb <-
        fil_lib_sop_pre_ecm
    },
    prepare_libraries_sop_hmdb = {
      yamls_params$prepare_libraries_sop_hmdb$files$libraries$sop$raw$hmdb <-
        fil_lib_sop_raw_hmd
      yamls_params$prepare_libraries_sop_hmdb$files$libraries$sop$prepared$hmdb <-
        fil_lib_sop_pre_hmd
    },
    prepare_libraries_sop_lotus = {
      yamls_params$prepare_libraries_sop_lotus$files$libraries$sop$raw$lotus <-
        fil_lib_sop_raw_lot
      yamls_params$prepare_libraries_sop_lotus$files$libraries$sop$prepared$lotus <-
        fil_lib_sop_pre_lot
    },
    prepare_libraries_sop_merged = {
      yamls_params$prepare_libraries_sop_merged$files$libraries$sop$prepared <-
        fil_lib_sop_pre
      yamls_params$prepare_libraries_sop_merged$files$libraries$sop$merged$keys <-
        fil_lib_sop_mer_key
      yamls_params$prepare_libraries_sop_merged$files$libraries$sop$merged$organisms$names <-
        fil_lib_sop_mer_org_nam
      yamls_params$prepare_libraries_sop_merged$files$libraries$sop$merged$organisms$taxonomies$ott <-
        fil_lib_sop_mer_org_tax_ott
      yamls_params$prepare_libraries_sop_merged$files$libraries$sop$merged$structures$stereo <-
        fil_lib_sop_mer_str_ste
      yamls_params$prepare_libraries_sop_merged$files$libraries$sop$merged$structures$metadata <-
        fil_lib_sop_mer_str_met
      yamls_params$prepare_libraries_sop_merged$files$libraries$sop$merged$structures$names <-
        fil_lib_sop_mer_str_nam
      yamls_params$prepare_libraries_sop_merged$files$libraries$sop$merged$structures$taxonomies$cla <-
        fil_lib_sop_mer_str_tax_cla
      yamls_params$prepare_libraries_sop_merged$files$libraries$sop$merged$structures$taxonomies$npc <-
        fil_lib_sop_mer_str_tax_npc
      yamls_params$prepare_libraries_sop_merged$organisms$filter$mode <-
        org_fil_mod
      yamls_params$prepare_libraries_sop_merged$organisms$filter$level <-
        org_fil_lev
      yamls_params$prepare_libraries_sop_merged$organisms$filter$value <-
        org_fil_val
    },
    prepare_libraries_spectra = {
      yamls_params$prepare_libraries_spectra$files$libraries$spectral$exp$neg <-
        fil_lib_spe_exp_neg
      yamls_params$prepare_libraries_spectra$files$libraries$spectral$exp$pos <-
        fil_lib_spe_exp_pos
      yamls_params$prepare_libraries_spectra$files$libraries$spectral$exp$raw <-
        fil_lib_spe_exp_raw
      yamls_params$prepare_libraries_spectra$files$libraries$spectral$is$neg <-
        fil_lib_spe_is_neg
      yamls_params$prepare_libraries_spectra$files$libraries$spectral$is$pos <-
        fil_lib_spe_is_pos
      yamls_params$prepare_libraries_spectra$files$libraries$spectral$is$raw <-
        fil_lib_spe_is_raw
      yamls_params$prepare_libraries_spectra$names$mgf$adduct <-
        names_mgf_ad
      yamls_params$prepare_libraries_spectra$names$mgf$collision_energy <-
        names_mgf_ce
      yamls_params$prepare_libraries_spectra$names$mgf$compound_id <-
        names_mgf_ci
      yamls_params$prepare_libraries_spectra$names$mgf$exact_mass <-
        names_mgf_em
      yamls_params$prepare_libraries_spectra$names$mgf$inchi <-
        names_mgf_in
      yamls_params$prepare_libraries_spectra$names$mgf$inchi_no_stereo <-
        names_mgf_io
      yamls_params$prepare_libraries_spectra$names$mgf$inchikey <-
        names_mgf_ik
      yamls_params$prepare_libraries_spectra$names$mgf$inchikey_no_stereo <-
        names_mgf_il
      yamls_params$prepare_libraries_spectra$names$mgf$molecular_formula <-
        names_mgf_mf
      yamls_params$prepare_libraries_spectra$names$mgf$name <-
        names_mgf_na
      yamls_params$prepare_libraries_spectra$names$mgf$polarity <-
        names_mgf_po
      yamls_params$prepare_libraries_spectra$names$mgf$smiles <-
        names_mgf_sm
      yamls_params$prepare_libraries_spectra$names$mgf$smiles_no_stereo <-
        names_mgf_sn
      yamls_params$prepare_libraries_spectra$names$mgf$spectrum_id <-
        names_mgf_si
      yamls_params$prepare_libraries_spectra$names$mgf$splash <-
        names_mgf_sp
      yamls_params$prepare_libraries_spectra$names$mgf$synonyms <-
        names_mgf_sy
      yamls_params$prepare_libraries_spectra$names$mgf$xlogp <-
        names_mgf_xl
    },
    prepare_taxa = {
      yamls_params$prepare_taxa$files$features$raw <-
        fil_fea_raw
      yamls_params$prepare_taxa$files$metadata$raw <-
        fil_met_raw
      yamls_params$prepare_taxa$files$metadata$prepared <-
        fil_met_pre
      yamls_params$prepare_taxa$files$libraries$sop$merged$organisms$taxonomies$ott <-
        fil_lib_sop_mer_org_tax_ott
      yamls_params$prepare_taxa$names$extension <-
        names_extension
      yamls_params$prepare_taxa$names$features <-
        names_features
      yamls_params$prepare_taxa$names$filename <-
        names_filename
      yamls_params$prepare_taxa$names$taxon <-
        names_taxon
      yamls_params$prepare_taxa$organisms$candidates <-
        org_can
      yamls_params$prepare_taxa$organisms$taxon <-
        org_tax
    },
    weight_annotations = {
      yamls_params$weight_annotations$annotations$candidates$final <-
        ann_can_fin
      yamls_params$weight_annotations$annotations$ms1only <-
        ann_ms1only
      yamls_params$weight_annotations$annotations$thresholds$consistency <-
        ann_thr_con
      yamls_params$weight_annotations$annotations$thresholds$ms1$biological <-
        ann_thr_ms1_bio
      yamls_params$weight_annotations$annotations$thresholds$ms1$chemical <-
        ann_thr_ms1_che
      yamls_params$weight_annotations$annotations$thresholds$ms1$condition <-
        ann_thr_ms1_con
      yamls_params$weight_annotations$files$pattern <-
        fil_pat
      yamls_params$weight_annotations$files$annotations$filtered <-
        fil_ann_fil
      yamls_params$weight_annotations$files$annotations$prepared$canopus <-
        fil_ann_pre_can
      yamls_params$weight_annotations$files$annotations$prepared$formula <-
        fil_ann_pre_for
      yamls_params$weight_annotations$files$annotations$processed <-
        fil_ann_pro
      yamls_params$weight_annotations$files$libraries$sop$merged$keys <-
        fil_lib_sop_mer_key
      yamls_params$weight_annotations$files$libraries$sop$merged$organisms$taxonomies$ott <-
        fil_lib_sop_mer_org_tax_ott
      yamls_params$weight_annotations$files$libraries$sop$merged$structures$stereo <-
        fil_lib_sop_mer_str_ste
      yamls_params$weight_annotations$files$networks$spectral$components$prepared <-
        fil_net_spe_com_pre
      yamls_params$weight_annotations$files$networks$spectral$edges$prepared <-
        fil_net_spe_edg_pre
      yamls_params$weight_annotations$files$metadata$prepared <-
        fil_met_pre
      yamls_params$weight_annotations$weights$global$biological <-
        wei_glo_bio
      yamls_params$weight_annotations$weights$global$chemical <-
        wei_glo_che
      yamls_params$weight_annotations$weights$global$spectral <-
        wei_glo_spe
      yamls_params$weight_annotations$weights$biological$domain <-
        wei_bio_01
      yamls_params$weight_annotations$weights$biological$kingdom <-
        wei_bio_02
      yamls_params$weight_annotations$weights$biological$phylum <-
        wei_bio_03
      yamls_params$weight_annotations$weights$biological$class <-
        wei_bio_04
      yamls_params$weight_annotations$weights$biological$order <-
        wei_bio_05
      yamls_params$weight_annotations$weights$biological$infraorder <-
        wei_bio_06
      yamls_params$weight_annotations$weights$biological$family <-
        wei_bio_07
      yamls_params$weight_annotations$weights$biological$subfamily <-
        wei_bio_08
      yamls_params$weight_annotations$weights$biological$tribe <-
        wei_bio_09
      yamls_params$weight_annotations$weights$biological$subtribe <-
        wei_bio_10
      yamls_params$weight_annotations$weights$biological$genus <-
        wei_bio_11
      yamls_params$weight_annotations$weights$biological$subgenus <-
        wei_bio_12
      yamls_params$weight_annotations$weights$biological$species <-
        wei_bio_13
      yamls_params$weight_annotations$weights$biological$subspecies <-
        wei_bio_14
      yamls_params$weight_annotations$weights$biological$variety <-
        wei_bio_15
      yamls_params$weight_annotations$weights$chemical$cla$kingdom <-
        wei_che_11
      yamls_params$weight_annotations$weights$chemical$npc$pathway <-
        wei_che_12
      yamls_params$weight_annotations$weights$chemical$cla$superclass <-
        wei_che_13
      yamls_params$weight_annotations$weights$chemical$npc$superclass <-
        wei_che_14
      yamls_params$weight_annotations$weights$chemical$cla$class <-
        wei_che_21
      yamls_params$weight_annotations$weights$chemical$npc$class <-
        wei_che_22
      yamls_params$weight_annotations$weights$chemical$cla$parent <-
        wei_che_23
      yamls_params$weight_annotations$options$compounds_names <-
        opt_cpd_nam
      yamls_params$weight_annotations$options$force <-
        opt_for
      yamls_params$weight_annotations$options$remove_ties <-
        opt_rem_tie
      yamls_params$weight_annotations$options$summarise <-
        opt_sum
    }
  )

  log_debug(x = "Changing filenames")
  switch(step,
    annotate_masses = {
      yamls_params$annotate_masses$files$annotations$prepared$structural <-
        yamls_params$annotate_masses$files$annotations$prepared$structural |>
        lapply(FUN = replace_id)
      yamls_params$annotate_masses$files$features$prepared <-
        yamls_params$annotate_masses$files$features$prepared |>
        lapply(FUN = replace_id)
      yamls_params$annotate_masses$files$networks$spectral$edges$raw <-
        yamls_params$annotate_masses$files$networks$spectral$edges$raw |>
        lapply(FUN = replace_id)
    },
    annotate_spectra = {
      yamls_params$annotate_spectra$files$annotations$raw$spectral$spectral <-
        yamls_params$annotate_spectra$files$annotations$raw$spectral$spectral |>
        lapply(FUN = replace_id)
      # yamls_params$annotate_spectra$files$spectral$raw <-
      #   yamls_params$annotate_spectra$files$spectral$raw |>
      #   lapply(FUN = replace_id)
    },
    create_edges_spectra = {
      yamls_params$create_edges_spectra$files$networks$spectral$edges$raw <-
        yamls_params$create_edges_spectra$files$networks$spectral$edges$raw |>
        lapply(FUN = replace_id)
      # yamls_params$create_edges_spectra$files$spectral$raw <-
      #   yamls_params$create_edges_spectra$files$spectral$raw |>
      #   lapply(FUN = replace_id)
    },
    create_components = {
      yamls_params$create_components$files$networks$spectral$edges$prepared <-
        yamls_params$create_components$files$networks$spectral$edges$prepared |>
        lapply(FUN = replace_id)
      yamls_params$create_components$files$networks$spectral$components$raw <-
        yamls_params$create_components$files$networks$spectral$components$raw |>
        lapply(FUN = replace_id)
    },
    filter_annotations = {
      yamls_params$filter_annotations$files$annotations$filtered <-
        yamls_params$filter_annotations$files$annotations$filtered |>
        lapply(FUN = replace_id)
      yamls_params$filter_annotations$files$annotations$prepared$structural$gnps <-
        yamls_params$filter_annotations$files$annotations$prepared$structural$gnps |>
        lapply(FUN = replace_id)
      yamls_params$filter_annotations$files$annotations$prepared$structural$ms1 <-
        yamls_params$filter_annotations$files$annotations$prepared$structural$ms1 |>
        lapply(FUN = replace_id)
      yamls_params$filter_annotations$files$annotations$prepared$structural$sirius <-
        yamls_params$filter_annotations$files$annotations$prepared$structural$sirius |>
        lapply(FUN = replace_id)
      yamls_params$filter_annotations$files$annotations$prepared$structural$spectral <-
        yamls_params$filter_annotations$files$annotations$prepared$structural$spectral |>
        lapply(FUN = replace_id)
      yamls_params$filter_annotations$files$features$prepared <-
        yamls_params$filter_annotations$files$features$prepared |>
        lapply(FUN = replace_id)
    },
    prepare_features_tables = {
      # yamls_params$prepare_features_tables$files$features$raw <-
      #   yamls_params$prepare_features_tables$files$features$raw |>
      #   lapply(FUN = replace_id)
      yamls_params$prepare_features_tables$files$features$prepared <-
        yamls_params$prepare_features_tables$files$features$prepared |>
        lapply(FUN = replace_id)
    },
    prepare_features_components = {
      yamls_params$prepare_features_components$files$networks$spectral$components$raw <-
        yamls_params$prepare_features_components$files$networks$spectral$components$raw |>
        lapply(FUN = replace_id)
      yamls_params$prepare_features_components$files$networks$spectral$components$prepared <-
        yamls_params$prepare_features_components$files$networks$spectral$components$prepared |>
        lapply(FUN = replace_id)
    },
    prepare_features_edges = {
      yamls_params$prepare_features_edges$files$networks$spectral$edges$raw$ms1 <-
        yamls_params$prepare_features_edges$files$networks$spectral$edges$raw$ms1 |>
        lapply(FUN = replace_id)
      yamls_params$prepare_features_edges$files$networks$spectral$edges$raw$spectral <-
        yamls_params$prepare_features_edges$files$networks$spectral$edges$raw$spectral |>
        lapply(FUN = replace_id)
      yamls_params$prepare_features_edges$files$networks$spectral$edges$prepared <-
        yamls_params$prepare_features_edges$files$networks$spectral$edges$prepared |>
        lapply(FUN = replace_id)
    },
    prepare_annotations_gnps = {
      yamls_params$prepare_annotations_gnps$files$annotations$raw$spectral$gnps <-
        yamls_params$prepare_annotations_gnps$files$annotations$raw$spectral$gnps |>
        lapply(FUN = replace_id)
      yamls_params$prepare_annotations_gnps$files$annotations$prepared$structural$gnps <-
        yamls_params$prepare_annotations_gnps$files$annotations$prepared$structural$gnps |>
        lapply(FUN = replace_id)
    },
    prepare_annotations_sirius = {
      # yamls_params$prepare_annotations_sirius$files$annotations$raw$sirius <-
      #   yamls_params$prepare_annotations_sirius$files$annotations$raw$sirius |>
      #   lapply(FUN = replace_id)
      yamls_params$prepare_annotations_sirius$files$annotations$prepared$canopus <-
        yamls_params$prepare_annotations_sirius$files$annotations$prepared$canopus |>
        lapply(FUN = replace_id)
      yamls_params$prepare_annotations_sirius$files$annotations$prepared$formula <-
        yamls_params$prepare_annotations_sirius$files$annotations$prepared$formula |>
        lapply(FUN = replace_id)
      yamls_params$prepare_annotations_sirius$files$annotations$prepared$structural <-
        yamls_params$prepare_annotations_sirius$files$annotations$prepared$structural |>
        lapply(FUN = replace_id)
    },
    prepare_annotations_spectra = {
      yamls_params$prepare_annotations_spectra$files$annotations$raw$spectral$spectral <-
        yamls_params$prepare_annotations_spectra$files$annotations$raw$spectral$spectral |>
        lapply(FUN = replace_id)
      yamls_params$prepare_annotations_spectra$files$annotations$prepared$structural <-
        yamls_params$prepare_annotations_spectra$files$annotations$prepared$structural |>
        lapply(FUN = replace_id)
    },
    prepare_taxa = {
      # yamls_params$prepare_taxa$files$features$raw <-
      #   yamls_params$prepare_taxa$files$features$raw |>
      #   lapply(FUN = replace_id)
      # yamls_params$prepare_taxa$files$metadata$raw <-
      #   yamls_params$prepare_taxa$files$metadata$raw |>
      #   lapply(FUN = replace_id)
      yamls_params$prepare_taxa$files$metadata$prepared <-
        yamls_params$prepare_taxa$files$metadata$prepared |>
        lapply(FUN = replace_id)
    },
    weight_annotations = {
      yamls_params$weight_annotations$files$annotations$filtered <-
        yamls_params$weight_annotations$files$annotations$filtered |>
        lapply(FUN = replace_id)
      yamls_params$weight_annotations$files$annotations$prepared$canopus <-
        yamls_params$weight_annotations$files$annotations$prepared$canopus |>
        lapply(FUN = replace_id)
      yamls_params$weight_annotations$files$annotations$prepared$formula <-
        yamls_params$weight_annotations$files$annotations$prepared$formula |>
        lapply(FUN = replace_id)
      yamls_params$weight_annotations$files$annotations$processed <-
        yamls_params$weight_annotations$files$annotations$processed |>
        lapply(FUN = replace_id)
      yamls_params$weight_annotations$files$features$prepared <-
        yamls_params$weight_annotations$files$features$prepared |>
        lapply(FUN = replace_id)
      yamls_params$weight_annotations$files$networks$spectral$components$prepared <-
        yamls_params$weight_annotations$files$networks$spectral$components$prepared |>
        lapply(FUN = replace_id)
      yamls_params$weight_annotations$files$networks$spectral$edges$prepared <-
        yamls_params$weight_annotations$files$networks$spectral$edges$prepared |>
        lapply(FUN = replace_id)
      yamls_params$weight_annotations$files$metadata$prepared <-
        yamls_params$weight_annotations$files$metadata$prepared |>
        lapply(FUN = replace_id)
    }
  )

  yaml_export <- list$yaml_files |>
    gsub(pattern = "default", replacement = "user", fixed = TRUE)
  names(yaml_export) <- list$yaml_names

  if (!is.na(step)) {
    ## The dollar is for steps having similar names separated by underscores
    yamls_params <-
      yamls_params[grepl(
        pattern = paste0(step[[1]], "$"),
        x = names(yamls_params),
        perl = TRUE
      )]
    ## The dot is for steps having similar names separated by underscores
    yaml_export <-
      yaml_export[grepl(
        pattern = paste0(step[[1]], "\\."),
        x = yaml_export,
        perl = TRUE
      )]
  }

  log_debug(x = "Exporting params ...")
  create_dir(export = yaml_export[[1]])
  # export_params(step = "prepare_params")
  lapply(
    X = seq_along(yamls_params),
    FUN = function(x) {
      yaml::write_yaml(
        x = yamls_params[[x]],
        file = yaml_export[x]
      )
    }
  )
  return(yaml_export)
}