diff isolib.R @ 0:8a1893635ac0 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/isolib.R	Tue Apr 23 06:39:20 2024 +0000
@@ -0,0 +1,80 @@
+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$formula
+  chemforms <- check_chemform(isotopes, chemforms)[, 2]
+
+  spectra <- data.frame()
+
+  for (current in adducts_to_use) {
+    adduct <- adducts[adducts$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()