annotate isolib.R @ 3:6b0fef8a77c0 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit bc3445f7c41271b0062c7674108f57708d08dd28

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]

    spectra <- data.frame()

    for (current in adducts_to_use) {
        adduct <- adducts[adducts$Name == current, ]
        multiplied_chemforms <- multiform(chemforms, adduct$Mult)

        if (adduct$Ion_mode == "negative") {
            merged_chemforms <- subform(multiplied_chemforms, adduct$Formula_ded)
        } else {
            merged_chemforms <- mergeform(multiplied_chemforms, adduct$Formula_add)
        }

        charge_string <- paste0(if (adduct$Charge > 0) "+" else "-", if (abs(adduct$Charge) > 1) abs(adduct$Charge) else "")
        adduct_string <- paste0("[", adduct$Name, "]", charge_string)
        precursor_mz <- calculateMass(multiplied_chemforms) + adduct$Mass

        if (args[4] == TRUE) {
            names <- paste(compound_table$name, paste0("(", adduct$Name, ")"), sep = " ")
        } else {
            names <- compound_table$name
        }

        spectra_df <- data.frame(
            name = names,
            adduct = adduct_string,
            formula = chemforms,
            charge = adduct$Charge,
            ionization_mode = adduct$Ion_mode,
            precursor_mz = precursor_mz,
            msLevel = as.integer(1)
        )

        if ("rt" %in% colnames(compound_table)) {
            spectra_df$retention_time <- compound_table$rt
        }

        patterns <- enviPat::isopattern(
            isotopes = isotopes,
            chemforms = merged_chemforms,
            charge = adduct$Charge,
            threshold = as.numeric(args[3]),
        )

        mzs <- list()
        intensities <- list()
        for (i in seq_along(patterns)) {
            mzs <- append(mzs, list(patterns[[i]][, 1]))
            intensities <- append(intensities, list(patterns[[i]][, 2]))
        }

        spectra_df$mz <- mzs
        spectra_df$intensity <- intensities
        spectra <- rbind(spectra, spectra_df)
    }

    sps <- Spectra(spectra)
    export(sps, MsBackendMsp(), file = args[5])
}

# Get the command line arguments
args <- commandArgs(trailingOnly = TRUE)
# Call the main function
main()