Prepare annotations SIRIUS

Description

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

library("tima")

copy_backbone()
go_to_cache()
prepare_annotations_sirius()
unlink("data", recursive = TRUE)