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Prepare annotations SIRIUS

Source: R/prepare_annotations_sirius.R
prepare_annotations_sirius.Rd

This function prepares Sirius results to make them compatible

Usage

prepare_annotations_sirius(
  input_directory = get_params(step =
    "prepare_annotations_sirius")$files$annotations$raw$sirius,
  output_ann = get_params(step =
    "prepare_annotations_sirius")$files$annotations$prepared$structural$sirius,
  output_can = get_params(step =
    "prepare_annotations_sirius")$files$annotations$prepared$canopus,
  output_for = get_params(step =
    "prepare_annotations_sirius")$files$annotations$prepared$formula,
  sirius_version = get_params(step = "prepare_annotations_sirius")$tools$sirius$version,
  str_stereo = get_params(step =
    "prepare_annotations_sirius")$files$libraries$sop$merged$structures$stereo,
  str_met = get_params(step =
    "prepare_annotations_sirius")$files$libraries$sop$merged$structures$metadata,
  str_nam = get_params(step =
    "prepare_annotations_sirius")$files$libraries$sop$merged$structures$names,
  str_tax_cla = get_params(step =
    "prepare_annotations_sirius")$files$libraries$sop$merged$structures$taxonomies$cla,
  str_tax_npc = get_params(step =
    "prepare_annotations_sirius")$files$libraries$sop$merged$structures$taxonomies$npc
)

Arguments

input_directory

Directory containing the Sirius results

output_ann

Output where to save prepared annotation results

output_can

Output where to save prepared canopus results

output_for

Output where to save prepared formula results

sirius_version

Sirius version

str_stereo

File containing structures stereo

str_met

File containing structures metadata

str_nam

File containing structures names

str_tax_cla

File containing Classyfire taxonomy

str_tax_npc

File containing NPClassifier taxonomy

Value

The path to the prepared SIRIUS annotations

Examples

if (FALSE) { # \dontrun{
tima:::copy_backbone()
go_to_cache()
prepare_annotations_sirius()
unlink("data", recursive = TRUE)
} # }