comparison isolib.R @ 2:b3251a7dae25 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit b9574494a6f9d2239dc81899e6d4074b33b078b7

1:7a4540275084

library(enviPat)
library(Spectra)
library(MsBackendMsp)
library(MetaboCoreUtils)

#' @param args A list of command line arguments.
main <- function() {
  data(isotopes)
  data(adducts)

  args <- commandArgs(trailingOnly = TRUE)
  compound_table <- read.delim(args[1], stringsAsFactors = FALSE)
  adducts_to_use <- c(unlist(strsplit(args[2], ",", fixed = TRUE)))

  chemforms <- compound_table$formula
  chemforms <- check_chemform(isotopes, chemforms)[, 2]

2:b3251a7dae25

library(enviPat)
library(Spectra)
library(MsBackendMsp)
library(MetaboCoreUtils)
library(readr)

#' @param args A list of command line arguments.
main <- function() {
  data(isotopes)
  data(adducts)

  args <- commandArgs(trailingOnly = TRUE)
  compound_table <- read_tsv(
    file = args[1],
    col_types = "ccd",
    col_select = tidyselect::all_of(c("name", "formula")) | tidyselect::any_of("rt")
  )
  adducts_to_use <- c(unlist(strsplit(args[2], ",", fixed = TRUE)))

  chemforms <- compound_table$formula
  chemforms <- check_chemform(isotopes, chemforms)[, 2]