diff --git a/DESCRIPTION b/DESCRIPTION
index c3ef33b2f..944fb7d16 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -50,6 +50,7 @@ Imports:
     tidyfst (>= 1.7.9),
     utils,
     visNetwork (>= 2.1.2),
+    withr (>= 3.0.0),
     yaml (>= 2.3.8)
 Suggests: 
     BiocManager,
diff --git a/codemeta.json b/codemeta.json
index f204c97ec..45c849a9e 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -563,6 +563,19 @@
       "sameAs": "https://CRAN.R-project.org/package=visNetwork"
     },
     "37": {
+      "@type": "SoftwareApplication",
+      "identifier": "withr",
+      "name": "withr",
+      "version": ">= 3.0.0",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=withr"
+    },
+    "38": {
       "@type": "SoftwareApplication",
       "identifier": "yaml",
       "name": "yaml",
@@ -578,7 +591,7 @@
     "SystemRequirements": null
   },
   "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
-  "fileSize": "4376.027KB",
+  "fileSize": "4377.449KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",
diff --git a/inst/app.R b/inst/app.R
index b2b0e1942..1332b1407 100644
--- a/inst/app.R
+++ b/inst/app.R
@@ -2070,18 +2070,18 @@ server <- function(input, output, session) {
 }
 url <- "<http://127.0.0.1:3838>"
 log_debug("Please, open:", url, "on your favorite browser, but not Edge.")
-shinyApp(
-  ui = ui,
-  server = server,
-  onStart = function() {
-    if (i_am_a_whale) {
-      message("I\'m inside the matrix ;(")
-      setwd(dir = "..")
-    } else {
-      cache <- fs::path_home(".tima")
-      fs::dir_create(cache)
-      message("Working in ", cache)
-      setwd(dir = cache)
-    }
-  }
-)
+dir <- if (i_am_a_whale) {
+  message("I\'m inside the matrix ;(")
+  ".."
+} else {
+  cache <- fs::path_home(".tima")
+  fs::dir_create(cache)
+  message("Working in ", cache)
+  cache
+}
+withr::with_dir(new = dir, code = {
+  shinyApp(
+    ui = ui,
+    server = server
+  )
+})
diff --git a/tests/testthat/test-functions.R b/tests/testthat/test-functions.R
index dd1e866dc..9cde85e69 100644
--- a/tests/testthat/test-functions.R
+++ b/tests/testthat/test-functions.R
@@ -1,665 +1,675 @@
 library(testthat)
 ## need to do all in one because of outputs needed in the same temp dir
 ## use fixtures instead in the future
-test_that(desc = "Test functions", code = {
-  install_latest_version()
-  setwd(fs::path_home(".tima"))
-  ## Prepare parameters
-  paths <- parse_yaml_paths()
-  params <- get_params(step = "prepare_params")
-  ## For all steps
-  params$organisms$taxon <- ""
-  prepare_params(params_small = params)
-  params$organisms$taxon <- "Gentiana lutea"
-  prepare_params(params_small = params)
-  prepare_params(step = "annotate_masses")
-  prepare_params(step = "annotate_spectra")
-  prepare_params(step = "create_components")
-  prepare_params(step = "create_edges_spectra")
-  prepare_params(step = "filter_annotations")
-  prepare_params(step = "prepare_annotations_gnps")
-  prepare_params(step = "prepare_annotations_sirius")
-  prepare_params(step = "prepare_annotations_spectra")
-  prepare_params(step = "prepare_features_components")
-  prepare_params(step = "prepare_features_edges")
-  prepare_params(step = "prepare_features_tables")
-  prepare_params(step = "prepare_libraries_rt")
-  prepare_params(step = "prepare_libraries_sop_closed")
-  prepare_params(step = "prepare_libraries_sop_ecmdb")
-  prepare_params(step = "prepare_libraries_sop_hmdb")
-  prepare_params(step = "prepare_libraries_sop_lotus")
-  prepare_params(step = "prepare_libraries_sop_merged")
-  prepare_params(step = "prepare_libraries_spectra")
-  prepare_params(step = "prepare_taxa")
-  prepare_params(step = "weight_annotations")
-
-  ## When previous params exist
-  prepare_params()
-
-  ## replace id
-  replace_id(
-    x = "example/123456_features.tsv",
-    user_gnps = "",
-    user_filename = "Foo"
-  )
-
-  ## Get all files
-  ### Features table
-  get_file(
-    url = paths$urls$examples$features,
-    export = paths$data$source$features
-  )
-  get_gnps_tables(
-    filename = "example",
-    path_features = paths$data$source$features,
-    path_metadata = paths$data$source$metadata,
-    path_spectra = paths$data$source$spectra,
-    gnps_job_id = params$gnps$id
-  )
-  ### Metadata table
-  get_file(
-    url = paths$urls$examples$metadata,
-    export = paths$data$source$metadata
-  )
-  get_file(
-    url = paths$urls$examples$metadata |>
-      gsub(pattern = ".tsv", replacement = "_unrecognized.tsv", fixed = TRUE),
-    export = paths$data$source$metadata |>
-      gsub(pattern = ".tsv", replacement = "_unrecognized.tsv", fixed = TRUE)
-  )
-  ## Other GNPS job id (without metadata)
-  get_gnps_tables(
-    filename = "other",
-    path_features = paths$data$source$features,
-    path_metadata = paths$data$source$metadata,
-    path_spectra = paths$data$source$spectra,
-    gnps_job_id = paths$gnps$example2
-  )
-  ## When no GNPS job ID and no metadata are given
-  get_gnps_tables(
-    filename = "noGNPS",
-    path_features = paths$data$source$features,
-    path_metadata = list(),
-    path_spectra = paths$data$source$spectra,
-    gnps_job_id = NULL
-  )
-  ## When GNPS job ID == ""
-  get_gnps_tables(
-    filename = "noNoGNPS",
-    path_features = paths$data$source$features,
-    path_metadata = NULL,
-    path_spectra = paths$data$source$spectra,
-    gnps_job_id = ""
-  )
-
-  ### Spectra
-  #### Mini version for tests
-  ## Not including it in else statement above on purpose
-  unlink(paths$data$source$spectra)
-  get_file(
-    url = paths$urls$examples$spectra_mini,
-    export = paths$data$source$spectra
-  )
-  ## Checking if file already exists
-  get_file(
-    url = paths$urls$examples$spectra_mini,
-    export = paths$data$source$spectra
-  )
-  get_file(
-    url = paths$urls$examples$spectra_ms1,
-    export = paths$data$source$spectra |>
-      gsub(
-        pattern = "example_spectra",
-        replacement = "example_spectra_ms1",
-        fixed = TRUE
-      )
-  )
-
-  ### Spectral library with rt
-  get_file(
-    url = paths$urls$examples$spectral_lib_mini$with_rt,
-    export = paths$data$source$libraries$spectra$exp$with_rt
-  )
-  ### Temporal library
-  get_file(
-    url = paths$urls$examples$lib_mini$rt,
-    export = paths$data$source$libraries$rt$example_mini
-  )
-
-  #### SIRIUS
-  ## mini version for tests
-  get_example_sirius()
-
-  ### Libraries
-  #### ECMDB
-  ## try exception because of external resource
-  fake_ecmdb(export = "fakeECMDB.json.zip")
-  tryCatch(
-    expr = {
-      get_file(
-        url = paths$urls$ecmdb$metabolites,
-        export = paths$data$source$libraries$sop$ecmdb
-      )
-    },
-    error = function(e) {
-      fake_ecmdb(export = paths$data$source$libraries$sop$ecmdb)
-    }
-  )
-
-  #### HMDB
-  fake_hmdb(export = "fakeHMDB.zip")
-  tryCatch(
-    expr = {
-      get_file(
-        url = paths$urls$hmdb$structures,
-        export = paths$data$source$libraries$sop$hmdb
+withr::with_dir(
+  new = fs::path_home(".tima"),
+  code = test_that(desc = "Test functions", code = {
+    install_latest_version()
+    ## Prepare parameters
+    paths <- parse_yaml_paths()
+    params <- get_params(step = "prepare_params")
+    ## For all steps
+    params$organisms$taxon <- ""
+    prepare_params(params_small = params)
+    params$organisms$taxon <- "Gentiana lutea"
+    prepare_params(params_small = params)
+    prepare_params(step = "annotate_masses")
+    prepare_params(step = "annotate_spectra")
+    prepare_params(step = "create_components")
+    prepare_params(step = "create_edges_spectra")
+    prepare_params(step = "filter_annotations")
+    prepare_params(step = "prepare_annotations_gnps")
+    prepare_params(step = "prepare_annotations_sirius")
+    prepare_params(step = "prepare_annotations_spectra")
+    prepare_params(step = "prepare_features_components")
+    prepare_params(step = "prepare_features_edges")
+    prepare_params(step = "prepare_features_tables")
+    prepare_params(step = "prepare_libraries_rt")
+    prepare_params(step = "prepare_libraries_sop_closed")
+    prepare_params(step = "prepare_libraries_sop_ecmdb")
+    prepare_params(step = "prepare_libraries_sop_hmdb")
+    prepare_params(step = "prepare_libraries_sop_lotus")
+    prepare_params(step = "prepare_libraries_sop_merged")
+    prepare_params(step = "prepare_libraries_spectra")
+    prepare_params(step = "prepare_taxa")
+    prepare_params(step = "weight_annotations")
+
+    ## When previous params exist
+    prepare_params()
+
+    ## replace id
+    replace_id(
+      x = "example/123456_features.tsv",
+      user_gnps = "",
+      user_filename = "Foo"
+    )
+
+    ## Get all files
+    ### Features table
+    get_file(
+      url = paths$urls$examples$features,
+      export = paths$data$source$features
+    )
+    get_gnps_tables(
+      filename = "example",
+      path_features = paths$data$source$features,
+      path_metadata = paths$data$source$metadata,
+      path_spectra = paths$data$source$spectra,
+      gnps_job_id = params$gnps$id
+    )
+    ### Metadata table
+    get_file(
+      url = paths$urls$examples$metadata,
+      export = paths$data$source$metadata
+    )
+    get_file(
+      url = paths$urls$examples$metadata |>
+        gsub(
+          pattern = ".tsv",
+          replacement = "_unrecognized.tsv",
+          fixed = TRUE
+        ),
+      export = paths$data$source$metadata |>
+        gsub(
+          pattern = ".tsv",
+          replacement = "_unrecognized.tsv",
+          fixed = TRUE
+        )
+    )
+    ## Other GNPS job id (without metadata)
+    get_gnps_tables(
+      filename = "other",
+      path_features = paths$data$source$features,
+      path_metadata = paths$data$source$metadata,
+      path_spectra = paths$data$source$spectra,
+      gnps_job_id = paths$gnps$example2
+    )
+    ## When no GNPS job ID and no metadata are given
+    get_gnps_tables(
+      filename = "noGNPS",
+      path_features = paths$data$source$features,
+      path_metadata = list(),
+      path_spectra = paths$data$source$spectra,
+      gnps_job_id = NULL
+    )
+    ## When GNPS job ID == ""
+    get_gnps_tables(
+      filename = "noNoGNPS",
+      path_features = paths$data$source$features,
+      path_metadata = NULL,
+      path_spectra = paths$data$source$spectra,
+      gnps_job_id = ""
+    )
+
+    ### Spectra
+    #### Mini version for tests
+    ## Not including it in else statement above on purpose
+    unlink(paths$data$source$spectra)
+    get_file(
+      url = paths$urls$examples$spectra_mini,
+      export = paths$data$source$spectra
+    )
+    ## Checking if file already exists
+    get_file(
+      url = paths$urls$examples$spectra_mini,
+      export = paths$data$source$spectra
+    )
+    get_file(
+      url = paths$urls$examples$spectra_ms1,
+      export = paths$data$source$spectra |>
+        gsub(
+          pattern = "example_spectra",
+          replacement = "example_spectra_ms1",
+          fixed = TRUE
+        )
+    )
+
+    ### Spectral library with rt
+    get_file(
+      url = paths$urls$examples$spectral_lib_mini$with_rt,
+      export = paths$data$source$libraries$spectra$exp$with_rt
+    )
+    ### Temporal library
+    get_file(
+      url = paths$urls$examples$lib_mini$rt,
+      export = paths$data$source$libraries$rt$example_mini
+    )
+
+    #### SIRIUS
+    ## mini version for tests
+    get_example_sirius()
+
+    ### Libraries
+    #### ECMDB
+    ## try exception because of external resource
+    fake_ecmdb(export = "fakeECMDB.json.zip")
+    tryCatch(
+      expr = {
+        get_file(
+          url = paths$urls$ecmdb$metabolites,
+          export = paths$data$source$libraries$sop$ecmdb
+        )
+      },
+      error = function(e) {
+        fake_ecmdb(export = paths$data$source$libraries$sop$ecmdb)
+      }
+    )
+
+    #### HMDB
+    fake_hmdb(export = "fakeHMDB.zip")
+    tryCatch(
+      expr = {
+        get_file(
+          url = paths$urls$hmdb$structures,
+          export = paths$data$source$libraries$sop$hmdb
+        )
+      },
+      error = function(e) {
+        fake_hmdb(export = paths$data$source$libraries$sop$hmdb)
+      }
+    )
+
+    #### LOTUS
+    ## try exception because of external resource
+    fake_lotus(export = "fakeLotus.csv.gz")
+    tryCatch(
+      expr = {
+        get_last_version_from_zenodo(
+          doi = paths$urls$lotus$doi,
+          pattern = paths$urls$lotus$pattern,
+          path = paths$data$source$libraries$sop$lotus
+        )
+      },
+      error = function(e) {
+        fake_lotus(export = paths$data$source$libraries$sop$lotus)
+      }
+    )
+    ## Check it does not download it a second time
+    ## try exception because of external resource
+    tryCatch(
+      expr = {
+        get_last_version_from_zenodo(
+          doi = paths$urls$lotus$doi,
+          pattern = paths$urls$lotus$pattern,
+          path = paths$data$source$libraries$sop$lotus
+        )
+      },
+      error = function(e) {
+        fake_lotus(export = paths$data$source$libraries$sop$lotus)
+      }
+    )
+
+    #### ISDB
+    ## smaller version for testing
+    # get_file(
+    #   url = paths$urls$examples$spectral_lib$pos,
+    #   export = paths$data$source$libraries$spectra$is$lotus$pos |>
+    #     gsub(
+    #       pattern = "isdb_pos.mgf",
+    #       replacement = "lotus_pos.rds",
+    #       fixed = TRUE
+    #     )
+    # )
+    get_file(
+      url = paths$urls$examples$spectral_lib_mini$pos,
+      export = paths$data$source$libraries$spectra$is$lotus$pos
+    )
+    # get_file(
+    #   url = paths$urls$examples$spectral_lib$neg,
+    #   export = paths$data$source$libraries$spectra$is$lotus$neg |>
+    #     gsub(
+    #       pattern = "isdb_neg.mgf",
+    #       replacement = "lotus_neg.rds",
+    #       fixed = TRUE
+    #     )
+    # )
+    get_file(
+      url = paths$urls$examples$spectral_lib_mini$neg,
+      export = paths$data$source$libraries$spectra$is$lotus$neg
+    )
+
+    #### MassBank
+    get_massbank_spectra()
+    ## test it does not download it a second time
+    get_massbank_spectra()
+
+    ## Prepare libraries
+    ### Spectra
+    #### LOTUS
+    col_args <- list(
+      col_ad = NULL,
+      col_ce = NULL,
+      col_ci = "FILENAME",
+      col_em = "EXACTMASS",
+      col_in = NULL,
+      col_io = "INCHI",
+      col_ik = NULL,
+      col_il = "NAME",
+      col_mf = "MOLECULAR_FORMULA",
+      col_na = NULL,
+      col_po = "IONMODE",
+      col_sm = NULL,
+      col_sn = "SMILES",
+      col_si = NULL,
+      col_sp = NULL,
+      col_sy = NULL,
+      col_xl = NULL
+    )
+    ##### mgf
+    do.call(
+      what = prepare_libraries_spectra,
+      args = c(
+        col_args,
+        input = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$raw[[2]] |>
+          gsub(
+            pattern = "lotus_pos.rds",
+            replacement = "isdb_pos.mgf",
+            fixed = TRUE
+          ),
+        output_pos = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$pos,
+        output_neg = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$neg
       )
-    },
-    error = function(e) {
-      fake_hmdb(export = paths$data$source$libraries$sop$hmdb)
-    }
-  )
-
-  #### LOTUS
-  ## try exception because of external resource
-  fake_lotus(export = "fakeLotus.csv.gz")
-  tryCatch(
-    expr = {
-      get_last_version_from_zenodo(
-        doi = paths$urls$lotus$doi,
-        pattern = paths$urls$lotus$pattern,
-        path = paths$data$source$libraries$sop$lotus
+    )
+    ##### Check the library already exists warning
+    do.call(
+      what = prepare_libraries_spectra,
+      args = c(
+        col_args,
+        input = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$raw[[2]] |>
+          gsub(
+            pattern = "lotus_pos.rds",
+            replacement = "isdb_pos.mgf",
+            fixed = TRUE
+          ),
+        output_pos = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$pos,
+        output_neg = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$neg
       )
-    },
-    error = function(e) {
-      fake_lotus(export = paths$data$source$libraries$sop$lotus)
-    }
-  )
-  ## Check it does not download it a second time
-  ## try exception because of external resource
-  tryCatch(
-    expr = {
-      get_last_version_from_zenodo(
-        doi = paths$urls$lotus$doi,
-        pattern = paths$urls$lotus$pattern,
-        path = paths$data$source$libraries$sop$lotus
+    )
+    ##### Without metadata
+    do.call(
+      what = prepare_libraries_spectra,
+      args = c(
+        col_args,
+        input = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$raw[[1]] |>
+          gsub(
+            pattern = "lotus_neg.rds",
+            replacement = "isdb_neg.mgf",
+            fixed = TRUE
+          ),
+        output_pos = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$pos,
+        output_neg = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$neg
       )
-    },
-    error = function(e) {
-      fake_lotus(export = paths$data$source$libraries$sop$lotus)
-    }
-  )
-
-  #### ISDB
-  ## smaller version for testing
-  # get_file(
-  #   url = paths$urls$examples$spectral_lib$pos,
-  #   export = paths$data$source$libraries$spectra$is$lotus$pos |>
-  #     gsub(
-  #       pattern = "isdb_pos.mgf",
-  #       replacement = "lotus_pos.rds",
-  #       fixed = TRUE
-  #     )
-  # )
-  get_file(
-    url = paths$urls$examples$spectral_lib_mini$pos,
-    export = paths$data$source$libraries$spectra$is$lotus$pos
-  )
-  # get_file(
-  #   url = paths$urls$examples$spectral_lib$neg,
-  #   export = paths$data$source$libraries$spectra$is$lotus$neg |>
-  #     gsub(
-  #       pattern = "isdb_neg.mgf",
-  #       replacement = "lotus_neg.rds",
-  #       fixed = TRUE
-  #     )
-  # )
-  get_file(
-    url = paths$urls$examples$spectral_lib_mini$neg,
-    export = paths$data$source$libraries$spectra$is$lotus$neg
-  )
-
-  #### MassBank
-  get_massbank_spectra()
-  ## test it does not download it a second time
-  get_massbank_spectra()
-
-  ## Prepare libraries
-  ### Spectra
-  #### LOTUS
-  col_args <- list(
-    col_ad = NULL,
-    col_ce = NULL,
-    col_ci = "FILENAME",
-    col_em = "EXACTMASS",
-    col_in = NULL,
-    col_io = "INCHI",
-    col_ik = NULL,
-    col_il = "NAME",
-    col_mf = "MOLECULAR_FORMULA",
-    col_na = NULL,
-    col_po = "IONMODE",
-    col_sm = NULL,
-    col_sn = "SMILES",
-    col_si = NULL,
-    col_sp = NULL,
-    col_sy = NULL,
-    col_xl = NULL
-  )
-  ##### mgf
-  do.call(
-    what = prepare_libraries_spectra,
-    args = c(
-      col_args,
-      input = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$raw[[2]] |>
-        gsub(pattern = "lotus_pos.rds", replacement = "isdb_pos.mgf", fixed = TRUE),
-      output_pos = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$pos,
-      output_neg = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$neg
-    )
-  )
-  ##### Check the library already exists warning
-  do.call(
-    what = prepare_libraries_spectra,
-    args = c(
-      col_args,
-      input = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$raw[[2]] |>
-        gsub(pattern = "lotus_pos.rds", replacement = "isdb_pos.mgf", fixed = TRUE),
-      output_pos = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$pos,
-      output_neg = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$neg
-    )
-  )
-  ##### Without metadata
-  do.call(
-    what = prepare_libraries_spectra,
-    args = c(
-      col_args,
-      input = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$raw[[1]] |>
-        gsub(pattern = "lotus_neg.rds", replacement = "isdb_neg.mgf", fixed = TRUE),
-      output_pos = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$pos,
-      output_neg = get_params(step = "prepare_libraries_spectra")$files$libraries$spectral$is$neg
-    )
-  )
-  #### If does not exist
-  prepare_libraries_spectra(
-    input = "doesNotExists.txt",
-    output_pos = "data/interim/libraries/spectra/exp/nope_pos.rds",
-    output_neg = "data/interim/libraries/spectra/exp/nope_neg.rds",
-  )
-  #### Classical
-  prepare_libraries_spectra()
-  #### Again
-  prepare_libraries_spectra()
-
-  ## for msp reading test
-  # Spectrum 1 fails
-  import_spectra(dir(system.file("extdata", package = "MsBackendMsp"), full.names = TRUE, pattern = "msp$")[8L])
-
-  #### HMDB
-  # prepare_isdb_hmdb()
-
-  #### Closed
-  # prepare_mona()
-
-  ### Retention time
-  prepare_libraries_rt(
-    mgf_exp = list(pos = paths$data$source$libraries$spectra$exp$with_rt),
-    temp_exp = paths$data$source$libraries$rt$example_mini
-  )
-  ## Check wrong SMILES
-  tidytable::tidytable(
-    "rt" = 0.1,
-    "smiles" = "wrongSMILES",
-    "inchikey" = NA
-  ) |>
-    tidytable::fwrite("data/source/libraries/rt/example_bad.tsv")
-  prepare_libraries_rt(
-    temp_exp = "data/source/libraries/rt/example_bad.tsv"
-  )
-  expect_warning(object = prepare_libraries_rt(temp_exp = "data/source/libraries/rt/example_bad.tsv"))
-
-  ### SOP
-  #### Closed
-  ## To do as if there was an input
-  prepare_libraries_sop_closed(input = paths$data$source$libraries$sop$lotus)
-  ## When there is no input
-  prepare_libraries_sop_closed()
-
-  #### ECMDB
-  ## To do as if there was an input
-  prepare_libraries_sop_ecmdb(input = "randomNonExistingFile")
-  ## When there is no input
-  prepare_libraries_sop_ecmdb()
-
-  #### HMDB
-  prepare_libraries_sop_hmdb(input = "randomNonExistingFile")
-  prepare_libraries_sop_hmdb()
-
-  #### LOTUS
-  ## If LOTUS download failed
-  prepare_libraries_sop_lotus(input = "randomNonExistingFile")
-  prepare_libraries_sop_lotus()
-
-  #### MERGED
-  prepare_libraries_sop_merged(
-    filter = TRUE,
-    level = "family",
-    value = "Simaroubaceae|Gentianaceae",
-    output_key = "data/interim/libraries/sop/merged/bitter.tsv.gz"
-  )
-  prepare_libraries_sop_merged()
-
-  ### Features
-  #### if no RT
-  tidytable::tidytable(
-    "row ID" = 1,
-    "row m/z" = 123.4567,
-    "sample.mzML Peak area" = 98765.43
-  ) |>
-    tidytable::fwrite("data/source/example_features_no_rt.csv")
-  prepare_features_tables(
-    features = "data/source/example_features_no_rt.csv",
-    output = "data/interim/features/example_features_no_rt.tsv.gz"
-  )
-  #### classical
-  prepare_features_tables()
-
-  ## Performing MS1 annotation
-  ## TODO improve this
-  calculate_mass_from_adduct(adduct_string = "[2M1-2H2O+NaCl+H]2+", mass = 123.456)
-  calculate_mass_from_adduct(adduct_string = "[M+Na]+", mass = 123.456)
-  calculate_mass_from_adduct(adduct_string = "[M+H]+", mass = 123.456)
-  calculate_mass_from_adduct(adduct_string = "[M+]+", mass = 123.456)
-  calculate_mass_from_adduct(adduct_string = "[M]+", mass = 123.456)
-  calculate_mass_from_adduct(adduct_string = "[2M1-C6H12O6 (hexose)+NaCl+H]2+", mass = 123.456)
-  calculate_mass_from_adduct(adduct_string = "[M-C6H14O7 (hexose-H2O)+H]+", mass = 123.456)
-
-  ### Negative and no RT
-  annotate_masses(
-    features = "data/interim/features/example_features_no_rt.tsv.gz",
-    filter_nitro = FALSE,
-    ## shallow tolerance to speed up tests
-    tolerance_ppm = 1,
-    tolerance_rt = 0.01,
-    ms_mode = "neg"
-  )
-  ### Positive
-  annotate_masses(
-    ## shallow tolerance to speed up tests
-    tolerance_ppm = 1,
-    tolerance_rt = 0.01,
-    ms_mode = "pos"
-  )
-
-  ## Performing MS2 annotation
-  ### Negative
-  annotate_spectra(
-    library = list(
-      neg = paths$data$source$libraries$spectra$exp$with_rt,
-      pos = paths$data$source$libraries$spectra$exp$with_rt
-    ),
-    ## shallow tolerance to speed up tests
-    ppm = 1,
-    dalton = 0.001,
-    polarity = "neg"
-  )
-  ### Empty
-  annotate_spectra(
-    library = list("data/interim/libraries/spectra/exp/nope_pos.rds")
-  )
-  ### Approx
-  annotate_spectra(
-    library = list(pos = paths$data$source$libraries$spectra$exp$with_rt),
-    ## shallow tolerance to speed up tests
-    ppm = 1,
-    dalton = 0.001,
-    threshold = 2,
-    approx = TRUE
-  )
-
-  ## Create MS2 based edges
-  create_edges_spectra( ## shallow tolerance to speed up tests
-    ppm = 1,
-    dalton = 0.001
-  )
-  ## if MS1 only
-  create_edges_spectra(
-    input = "data/source/example_spectra_ms1.mgf",
-    ## shallow tolerance to speed up tests
-    ppm = 1,
-    dalton = 0.001
-  )
-
-  ### GNPS results
-  prepare_annotations_gnps(input = "fileDoesNotExist")
-  prepare_annotations_gnps(input = NULL)
-  prepare_annotations_gnps()
-
-  ### SIRIUS results
-  prepare_annotations_sirius(input_directory = NULL)
-  prepare_annotations_sirius(input_directory = "randomDirThatDoesNotExist")
-  ## When there is an input
-  prepare_annotations_sirius(
-    input_directory =
-      get_params(step = "prepare_annotations_sirius")$files$annotations$raw$sirius,
-  )
-  prepare_annotations_sirius(
-    input_directory = "data/interim/annotations/example_sirius.zip",
-    sirius_version = 5
-  )
-
-  ### ISDB results
-  prepare_annotations_spectra()
-
-  ### Edges
-  prepare_features_edges()
-
-  ## Create components
-  create_components()
-
-  ### Features components
-  prepare_features_components()
-
-  ### Taxa
-  ## Forcing all features to a single source organism
-  prepare_taxa(taxon = "Homo sapiens")
-  ## When empty
-  prepare_taxa(taxon = "")
-  ## Without file extension in the column names
-  prepare_taxa(extension = FALSE)
-  ## Testing for unrecognized taxa
-  prepare_taxa(
-    metadata = paths$data$source$metadata |>
-      gsub(pattern = ".tsv", replacement = "_unrecognized.tsv", fixed = TRUE)
-  )
-  ## Attributing based on intensity (multiple source organisms)
-  prepare_taxa()
-  ## Tests for ott API
-  fake_taxon_df <- data.frame("organism" = "Gentiana lutea")
-  wrong_taxon_df <- data.frame("organism" = "Gentiano luteo")
-  get_organism_taxonomy_ott(df = fake_taxon_df)
-  get_organism_taxonomy_ott(df = wrong_taxon_df)
-  get_organism_taxonomy_ott(
-    df = fake_taxon_df,
-    url = "https://api.opentreeoflife.org/v3/taxonomy/fakeDown"
-  )
-  ## Stupid tests for benchmark
-  data.frame(feature_id = 1, organism_name = "Gentiana lutea") |>
-    export_output("data/interim/benchmark/bench_test_in.tsv.gz")
-  taxize_spectra_benchmark(
-    input = "data/interim/benchmark/bench_test_in.tsv.gz",
-    keys = paths$data$interim$libraries$sop$merged$keys,
-    org_tax_ott =
-      get_params(step = "prepare_taxa")$files$libraries$sop$merged$organisms$taxonomies$ott,
-    output = "data/interim/benchmark/bench_test_out.tsv.gz"
-  )
-
-  ## Filter annotations
-  ## case when no RT lib
-  filter_annotations(rts = list())
-  filter_annotations()
-
-  ## Perform TIMA
-  ### Normal
-  weight_annotations(
-    candidates_final = 1,
-    minimal_ms1_bio = 0.8
-  )
-  ### Only MS1
-  weight_annotations(
-    ms1_only = TRUE,
-    remove_ties = TRUE,
-    summarise = TRUE,
-    candidates_final = 1,
-    minimal_ms1_bio = 0.8,
-    minimal_ms1_condition = "AND",
-    compounds_names = TRUE
-  )
-
-  ## CLI arguments check
-  arguments <- character()
-  arguments$ann_can_fin <- "x"
-  arguments$ann_ms1only <- "x"
-  arguments$ann_ms2_app <- "x"
-  arguments$ann_thr_con <- "x"
-  arguments$ann_thr_ms1_bio <- "x"
-  arguments$ann_thr_ms1_che <- "x"
-  arguments$ann_thr_ms1_con <- "x"
-  arguments$ann_thr_ms2_sim_ann <- "x"
-  arguments$ann_thr_ms2_sim_edg <- "x"
-  arguments$fil_pat <- "x"
-  arguments$fil_ann_raw_spe <- "x"
-  arguments$fil_ann_raw_spe_gnp <- "x"
-  arguments$fil_ann_raw_spe_spe <- "x"
-  arguments$fil_ann_raw_sir <- "x"
-  arguments$fil_ann_pre_can <- "x"
-  arguments$fil_ann_pre_for <- "x"
-  arguments$fil_ann_pre_str <- "x"
-  arguments$fil_ann_fil <- "x"
-  arguments$fil_ann_pro <- "x"
-  arguments$fil_fea_raw <- "x"
-  arguments$fil_fea_pre <- "x"
-  arguments$fil_lib_sop_raw_clo <- "x"
-  arguments$fil_lib_sop_raw_ecm <- "x"
-  arguments$fil_lib_sop_raw_hmd <- "x"
-  arguments$fil_lib_sop_raw_lot <- "x"
-  arguments$fil_lib_sop_pre <- "x"
-  arguments$fil_lib_spe_exp_neg <- "x"
-  arguments$fil_lib_spe_exp_pos <- "x"
-  arguments$fil_lib_spe_exp_raw <- "x"
-  arguments$fil_lib_spe_is_neg <- "x"
-  arguments$fil_lib_spe_is_pos <- "x"
-  arguments$fil_lib_spe_is_raw <- "x"
-  arguments$fil_lib_tem_exp_csv <- "x"
-  arguments$fil_lib_tem_exp_mgf_neg <- "x"
-  arguments$fil_lib_tem_exp_mgf_pos <- "x"
-  arguments$fil_lib_tem_is_csv <- "x"
-  arguments$fil_lib_tem_is_mgf_neg <- "x"
-  arguments$fil_lib_tem_is_mgf_pos <- "x"
-  arguments$fil_lib_tem_pre <- "x"
-  arguments$fil_net_spe_edg_raw <- "x"
-  arguments$fil_net_spe_edg_pre <- "x"
-  arguments$fil_net_spe_com_raw <- "x"
-  arguments$fil_net_spe_com_pre <- "x"
-  arguments$fil_met_raw <- "x"
-  arguments$fil_met_pre <- "x"
-  arguments$fil_spe_raw <- "x"
-  arguments$gnps_id <- "x"
-  arguments$gnps_workflow <- "x"
-  arguments$ms_add_neg <- "x"
-  arguments$ms_add_pos <- "x"
-  arguments$ms_clu_neg <- "x"
-  arguments$ms_clu_pos <- "x"
-  arguments$ms_pol <- "x"
-  arguments$ms_thr_ms1_int <- "x"
-  arguments$ms_thr_ms2_int <- "x"
-  arguments$ms_tol_mas_ppm_ms1 <- "x"
-  arguments$ms_tol_mas_ppm_ms2 <- "x"
-  arguments$ms_tol_mas_dal_ms1 <- "x"
-  arguments$ms_tol_mas_dal_ms2 <- "x"
-  arguments$ms_tol_rt_min <- "x"
-  arguments$names_adduct <- "x"
-  arguments$names_extension <- "x"
-  arguments$names_features <- "x"
-  arguments$names_filename <- "x"
-  arguments$names_inchikey <- "x"
-  arguments$names_mgf_ad <- "x"
-  arguments$names_mgf_ce <- "x"
-  arguments$names_mgf_ci <- "x"
-  arguments$names_mgf_em <- "x"
-  arguments$names_mgf_in <- "x"
-  arguments$names_mgf_io <- "x"
-  arguments$names_mgf_ik <- "x"
-  arguments$names_mgf_il <- "x"
-  arguments$names_mgf_mf <- "x"
-  arguments$names_mgf_na <- "x"
-  arguments$names_mgf_po <- "x"
-  # arguments$names_mgf_pc <- "x"
-  # arguments$names_mgf_pm <- "x"
-  arguments$names_mgf_sm <- "x"
-  arguments$names_mgf_sn <- "x"
-  arguments$names_mgf_si <- "x"
-  arguments$names_mgf_sp <- "x"
-  arguments$names_mgf_sy <- "x"
-  arguments$names_mgf_xl <- "x"
-  arguments$names_precursor <- "x"
-  arguments$names_rt <- "x"
-  arguments$names_rt_fea <- "x"
-  arguments$names_rt_lib <- "x"
-  arguments$names_smiles <- "x"
-  arguments$names_source <- "x"
-  arguments$names_target <- "x"
-  arguments$names_taxon <- "x"
-  arguments$org_can <- "x"
-  arguments$org_fil_mod <- "x"
-  arguments$org_fil_lev <- "x"
-  arguments$org_fil_val <- "x"
-  arguments$org_tax <- "x"
-  arguments$too_met <- "x"
-  arguments$too_net_spe_com <- "x"
-  arguments$too_net_spe_edg <- "x"
-  arguments$too_tax_bio <- "x"
-  arguments$too_tax_che <- "x"
-  arguments$units_rt <- "x"
-  arguments$wei_glo_bio <- "x"
-  arguments$wei_glo_che <- "x"
-  arguments$wei_glo_spe <- "x"
-  arguments$wei_bio_01 <- "x"
-  arguments$wei_bio_02 <- "x"
-  arguments$wei_bio_03 <- "x"
-  arguments$wei_bio_04 <- "x"
-  arguments$wei_bio_05 <- "x"
-  arguments$wei_bio_06 <- "x"
-  arguments$wei_bio_07 <- "x"
-  arguments$wei_bio_08 <- "x"
-  arguments$wei_bio_09 <- "x"
-  arguments$wei_bio_10 <- "x"
-  arguments$wei_bio_11 <- "x"
-  arguments$wei_bio_12 <- "x"
-  arguments$wei_bio_13 <- "x"
-  arguments$wei_bio_14 <- "x"
-  arguments$wei_bio_15 <- "x"
-  arguments$wei_che_11 <- "x"
-  arguments$wei_che_12 <- "x"
-  arguments$wei_che_13 <- "x"
-  arguments$wei_che_14 <- "x"
-  arguments$wei_che_21 <- "x"
-  arguments$wei_che_22 <- "x"
-  arguments$wei_che_23 <- "x"
-  arguments$compounds_names <- "x"
-  arguments$force <- "x"
-  arguments$nit_rul <- "x"
-  arguments$remove_ties <- "x"
-  arguments$summarise <- "x"
-
-  # Useless
-  keep_peaks(x = 0, prop = 0)
-  normalize_peaks()
-  remove_above_precursor()
-
-  parse_cli_params(
-    arguments = arguments,
-    parameters = params
-  )
-
-  succeed()
-})
+    )
+    #### If does not exist
+    prepare_libraries_spectra(
+      input = "doesNotExists.txt",
+      output_pos = "data/interim/libraries/spectra/exp/nope_pos.rds",
+      output_neg = "data/interim/libraries/spectra/exp/nope_neg.rds",
+    )
+    #### Classical
+    prepare_libraries_spectra()
+    #### Again
+    prepare_libraries_spectra()
+
+    ## for msp reading test
+    # Spectrum 1 fails
+    import_spectra(dir(
+      system.file("extdata", package = "MsBackendMsp"),
+      full.names = TRUE,
+      pattern = "msp$"
+    )[8L])
+
+    #### HMDB
+    # prepare_isdb_hmdb()
+
+    #### Closed
+    # prepare_mona()
+
+    ### Retention time
+    prepare_libraries_rt(
+      mgf_exp = list(pos = paths$data$source$libraries$spectra$exp$with_rt),
+      temp_exp = paths$data$source$libraries$rt$example_mini
+    )
+    ## Check wrong SMILES
+    tidytable::tidytable(
+      "rt" = 0.1,
+      "smiles" = "wrongSMILES",
+      "inchikey" = NA
+    ) |>
+      tidytable::fwrite("data/source/libraries/rt/example_bad.tsv")
+    prepare_libraries_rt(temp_exp = "data/source/libraries/rt/example_bad.tsv")
+    expect_warning(object = prepare_libraries_rt(temp_exp = "data/source/libraries/rt/example_bad.tsv"))
+
+    ### SOP
+    #### Closed
+    ## To do as if there was an input
+    prepare_libraries_sop_closed(input = paths$data$source$libraries$sop$lotus)
+    ## When there is no input
+    prepare_libraries_sop_closed()
+
+    #### ECMDB
+    ## To do as if there was an input
+    prepare_libraries_sop_ecmdb(input = "randomNonExistingFile")
+    ## When there is no input
+    prepare_libraries_sop_ecmdb()
+
+    #### HMDB
+    prepare_libraries_sop_hmdb(input = "randomNonExistingFile")
+    prepare_libraries_sop_hmdb()
+
+    #### LOTUS
+    ## If LOTUS download failed
+    prepare_libraries_sop_lotus(input = "randomNonExistingFile")
+    prepare_libraries_sop_lotus()
+
+    #### MERGED
+    prepare_libraries_sop_merged(
+      filter = TRUE,
+      level = "family",
+      value = "Simaroubaceae|Gentianaceae",
+      output_key = "data/interim/libraries/sop/merged/bitter.tsv.gz"
+    )
+    prepare_libraries_sop_merged()
+
+    ### Features
+    #### if no RT
+    tidytable::tidytable(
+      "row ID" = 1,
+      "row m/z" = 123.4567,
+      "sample.mzML Peak area" = 98765.43
+    ) |>
+      tidytable::fwrite("data/source/example_features_no_rt.csv")
+    prepare_features_tables(features = "data/source/example_features_no_rt.csv", output = "data/interim/features/example_features_no_rt.tsv.gz")
+    #### classical
+    prepare_features_tables()
+
+    ## Performing MS1 annotation
+    ## TODO improve this
+    calculate_mass_from_adduct(adduct_string = "[2M1-2H2O+NaCl+H]2+", mass = 123.456)
+    calculate_mass_from_adduct(adduct_string = "[M+Na]+", mass = 123.456)
+    calculate_mass_from_adduct(adduct_string = "[M+H]+", mass = 123.456)
+    calculate_mass_from_adduct(adduct_string = "[M+]+", mass = 123.456)
+    calculate_mass_from_adduct(adduct_string = "[M]+", mass = 123.456)
+    calculate_mass_from_adduct(adduct_string = "[2M1-C6H12O6 (hexose)+NaCl+H]2+", mass = 123.456)
+    calculate_mass_from_adduct(adduct_string = "[M-C6H14O7 (hexose-H2O)+H]+", mass = 123.456)
+
+    ### Negative and no RT
+    annotate_masses(
+      features = "data/interim/features/example_features_no_rt.tsv.gz",
+      filter_nitro = FALSE,
+      ## shallow tolerance to speed up tests
+      tolerance_ppm = 1,
+      tolerance_rt = 0.01,
+      ms_mode = "neg"
+    )
+    ### Positive
+    annotate_masses(
+      ## shallow tolerance to speed up tests
+      tolerance_ppm = 1,
+      tolerance_rt = 0.01,
+      ms_mode = "pos"
+    )
+
+    ## Performing MS2 annotation
+    ### Negative
+    annotate_spectra(
+      library = list(
+        neg = paths$data$source$libraries$spectra$exp$with_rt,
+        pos = paths$data$source$libraries$spectra$exp$with_rt
+      ),
+      ## shallow tolerance to speed up tests
+      ppm = 1,
+      dalton = 0.001,
+      polarity = "neg"
+    )
+    ### Empty
+    annotate_spectra(library = list("data/interim/libraries/spectra/exp/nope_pos.rds"))
+    ### Approx
+    annotate_spectra(
+      library = list(pos = paths$data$source$libraries$spectra$exp$with_rt),
+      ## shallow tolerance to speed up tests
+      ppm = 1,
+      dalton = 0.001,
+      threshold = 2,
+      approx = TRUE
+    )
+
+    ## Create MS2 based edges
+    create_edges_spectra( ## shallow tolerance to speed up tests
+      ppm = 1, dalton = 0.001
+    )
+    ## if MS1 only
+    create_edges_spectra(
+      input = "data/source/example_spectra_ms1.mgf",
+      ## shallow tolerance to speed up tests
+      ppm = 1,
+      dalton = 0.001
+    )
+
+    ### GNPS results
+    prepare_annotations_gnps(input = "fileDoesNotExist")
+    prepare_annotations_gnps(input = NULL)
+    prepare_annotations_gnps()
+
+    ### SIRIUS results
+    prepare_annotations_sirius(input_directory = NULL)
+    prepare_annotations_sirius(input_directory = "randomDirThatDoesNotExist")
+    ## When there is an input
+    prepare_annotations_sirius(
+      input_directory =
+        get_params(step = "prepare_annotations_sirius")$files$annotations$raw$sirius,
+    )
+    prepare_annotations_sirius(input_directory = "data/interim/annotations/example_sirius.zip", sirius_version = 5)
+
+    ### ISDB results
+    prepare_annotations_spectra()
+
+    ### Edges
+    prepare_features_edges()
+
+    ## Create components
+    create_components()
+
+    ### Features components
+    prepare_features_components()
+
+    ### Taxa
+    ## Forcing all features to a single source organism
+    prepare_taxa(taxon = "Homo sapiens")
+    ## When empty
+    prepare_taxa(taxon = "")
+    ## Without file extension in the column names
+    prepare_taxa(extension = FALSE)
+    ## Testing for unrecognized taxa
+    prepare_taxa(
+      metadata = paths$data$source$metadata |>
+        gsub(
+          pattern = ".tsv",
+          replacement = "_unrecognized.tsv",
+          fixed = TRUE
+        )
+    )
+    ## Attributing based on intensity (multiple source organisms)
+    prepare_taxa()
+    ## Tests for ott API
+    fake_taxon_df <- data.frame("organism" = "Gentiana lutea")
+    wrong_taxon_df <- data.frame("organism" = "Gentiano luteo")
+    get_organism_taxonomy_ott(df = fake_taxon_df)
+    get_organism_taxonomy_ott(df = wrong_taxon_df)
+    get_organism_taxonomy_ott(df = fake_taxon_df, url = "https://api.opentreeoflife.org/v3/taxonomy/fakeDown")
+    ## Stupid tests for benchmark
+    data.frame(feature_id = 1, organism_name = "Gentiana lutea") |>
+      export_output("data/interim/benchmark/bench_test_in.tsv.gz")
+    taxize_spectra_benchmark(
+      input = "data/interim/benchmark/bench_test_in.tsv.gz",
+      keys = paths$data$interim$libraries$sop$merged$keys,
+      org_tax_ott =
+        get_params(step = "prepare_taxa")$files$libraries$sop$merged$organisms$taxonomies$ott,
+      output = "data/interim/benchmark/bench_test_out.tsv.gz"
+    )
+
+    ## Filter annotations
+    ## case when no RT lib
+    filter_annotations(rts = list())
+    filter_annotations()
+
+    ## Perform TIMA
+    ### Normal
+    weight_annotations(candidates_final = 1, minimal_ms1_bio = 0.8)
+    ### Only MS1
+    weight_annotations(
+      ms1_only = TRUE,
+      remove_ties = TRUE,
+      summarise = TRUE,
+      candidates_final = 1,
+      minimal_ms1_bio = 0.8,
+      minimal_ms1_condition = "AND",
+      compounds_names = TRUE
+    )
+
+    ## CLI arguments check
+    arguments <- character()
+    arguments$ann_can_fin <- "x"
+    arguments$ann_ms1only <- "x"
+    arguments$ann_ms2_app <- "x"
+    arguments$ann_thr_con <- "x"
+    arguments$ann_thr_ms1_bio <- "x"
+    arguments$ann_thr_ms1_che <- "x"
+    arguments$ann_thr_ms1_con <- "x"
+    arguments$ann_thr_ms2_sim_ann <- "x"
+    arguments$ann_thr_ms2_sim_edg <- "x"
+    arguments$fil_pat <- "x"
+    arguments$fil_ann_raw_spe <- "x"
+    arguments$fil_ann_raw_spe_gnp <- "x"
+    arguments$fil_ann_raw_spe_spe <- "x"
+    arguments$fil_ann_raw_sir <- "x"
+    arguments$fil_ann_pre_can <- "x"
+    arguments$fil_ann_pre_for <- "x"
+    arguments$fil_ann_pre_str <- "x"
+    arguments$fil_ann_fil <- "x"
+    arguments$fil_ann_pro <- "x"
+    arguments$fil_fea_raw <- "x"
+    arguments$fil_fea_pre <- "x"
+    arguments$fil_lib_sop_raw_clo <- "x"
+    arguments$fil_lib_sop_raw_ecm <- "x"
+    arguments$fil_lib_sop_raw_hmd <- "x"
+    arguments$fil_lib_sop_raw_lot <- "x"
+    arguments$fil_lib_sop_pre <- "x"
+    arguments$fil_lib_spe_exp_neg <- "x"
+    arguments$fil_lib_spe_exp_pos <- "x"
+    arguments$fil_lib_spe_exp_raw <- "x"
+    arguments$fil_lib_spe_is_neg <- "x"
+    arguments$fil_lib_spe_is_pos <- "x"
+    arguments$fil_lib_spe_is_raw <- "x"
+    arguments$fil_lib_tem_exp_csv <- "x"
+    arguments$fil_lib_tem_exp_mgf_neg <- "x"
+    arguments$fil_lib_tem_exp_mgf_pos <- "x"
+    arguments$fil_lib_tem_is_csv <- "x"
+    arguments$fil_lib_tem_is_mgf_neg <- "x"
+    arguments$fil_lib_tem_is_mgf_pos <- "x"
+    arguments$fil_lib_tem_pre <- "x"
+    arguments$fil_net_spe_edg_raw <- "x"
+    arguments$fil_net_spe_edg_pre <- "x"
+    arguments$fil_net_spe_com_raw <- "x"
+    arguments$fil_net_spe_com_pre <- "x"
+    arguments$fil_met_raw <- "x"
+    arguments$fil_met_pre <- "x"
+    arguments$fil_spe_raw <- "x"
+    arguments$gnps_id <- "x"
+    arguments$gnps_workflow <- "x"
+    arguments$ms_add_neg <- "x"
+    arguments$ms_add_pos <- "x"
+    arguments$ms_clu_neg <- "x"
+    arguments$ms_clu_pos <- "x"
+    arguments$ms_pol <- "x"
+    arguments$ms_thr_ms1_int <- "x"
+    arguments$ms_thr_ms2_int <- "x"
+    arguments$ms_tol_mas_ppm_ms1 <- "x"
+    arguments$ms_tol_mas_ppm_ms2 <- "x"
+    arguments$ms_tol_mas_dal_ms1 <- "x"
+    arguments$ms_tol_mas_dal_ms2 <- "x"
+    arguments$ms_tol_rt_min <- "x"
+    arguments$names_adduct <- "x"
+    arguments$names_extension <- "x"
+    arguments$names_features <- "x"
+    arguments$names_filename <- "x"
+    arguments$names_inchikey <- "x"
+    arguments$names_mgf_ad <- "x"
+    arguments$names_mgf_ce <- "x"
+    arguments$names_mgf_ci <- "x"
+    arguments$names_mgf_em <- "x"
+    arguments$names_mgf_in <- "x"
+    arguments$names_mgf_io <- "x"
+    arguments$names_mgf_ik <- "x"
+    arguments$names_mgf_il <- "x"
+    arguments$names_mgf_mf <- "x"
+    arguments$names_mgf_na <- "x"
+    arguments$names_mgf_po <- "x"
+    # arguments$names_mgf_pc <- "x"
+    # arguments$names_mgf_pm <- "x"
+    arguments$names_mgf_sm <- "x"
+    arguments$names_mgf_sn <- "x"
+    arguments$names_mgf_si <- "x"
+    arguments$names_mgf_sp <- "x"
+    arguments$names_mgf_sy <- "x"
+    arguments$names_mgf_xl <- "x"
+    arguments$names_precursor <- "x"
+    arguments$names_rt <- "x"
+    arguments$names_rt_fea <- "x"
+    arguments$names_rt_lib <- "x"
+    arguments$names_smiles <- "x"
+    arguments$names_source <- "x"
+    arguments$names_target <- "x"
+    arguments$names_taxon <- "x"
+    arguments$org_can <- "x"
+    arguments$org_fil_mod <- "x"
+    arguments$org_fil_lev <- "x"
+    arguments$org_fil_val <- "x"
+    arguments$org_tax <- "x"
+    arguments$too_met <- "x"
+    arguments$too_net_spe_com <- "x"
+    arguments$too_net_spe_edg <- "x"
+    arguments$too_tax_bio <- "x"
+    arguments$too_tax_che <- "x"
+    arguments$units_rt <- "x"
+    arguments$wei_glo_bio <- "x"
+    arguments$wei_glo_che <- "x"
+    arguments$wei_glo_spe <- "x"
+    arguments$wei_bio_01 <- "x"
+    arguments$wei_bio_02 <- "x"
+    arguments$wei_bio_03 <- "x"
+    arguments$wei_bio_04 <- "x"
+    arguments$wei_bio_05 <- "x"
+    arguments$wei_bio_06 <- "x"
+    arguments$wei_bio_07 <- "x"
+    arguments$wei_bio_08 <- "x"
+    arguments$wei_bio_09 <- "x"
+    arguments$wei_bio_10 <- "x"
+    arguments$wei_bio_11 <- "x"
+    arguments$wei_bio_12 <- "x"
+    arguments$wei_bio_13 <- "x"
+    arguments$wei_bio_14 <- "x"
+    arguments$wei_bio_15 <- "x"
+    arguments$wei_che_11 <- "x"
+    arguments$wei_che_12 <- "x"
+    arguments$wei_che_13 <- "x"
+    arguments$wei_che_14 <- "x"
+    arguments$wei_che_21 <- "x"
+    arguments$wei_che_22 <- "x"
+    arguments$wei_che_23 <- "x"
+    arguments$compounds_names <- "x"
+    arguments$force <- "x"
+    arguments$nit_rul <- "x"
+    arguments$remove_ties <- "x"
+    arguments$summarise <- "x"
+
+    # Useless
+    keep_peaks(x = 0, prop = 0)
+    normalize_peaks()
+    remove_above_precursor()
+
+    parse_cli_params(arguments = arguments, parameters = params)
+
+    succeed()
+  })
+)