diff CAMERA_findIsotopes.R @ 0:a8aa53d54c88 draft default tip

planemo upload commit 24d44ee26b7c23380c2b42fae2f7f6e58472100d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CAMERA_findIsotopes.R	Sun Nov 24 21:30:26 2024 +0000
@@ -0,0 +1,138 @@
+#!/usr/bin/env Rscript
+
+# ----- PACKAGE -----
+cat("\tSESSION INFO\n")
+
+# Import the different functions
+source_local <- function(fname) {
+  argv <- commandArgs(trailingOnly = FALSE)
+  base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+  source(paste(base_dir, fname, sep = "/"))
+}
+source_local("lib.r")
+
+pkgs <- c("CAMERA", "xcms", "multtest", "batch")
+loadAndDisplayPackages(pkgs)
+cat("\n\n")
+# ----- ARGUMENTS -----
+cat("\tARGUMENTS INFO\n")
+
+args <- parseCommandArgs(evaluate = FALSE) # interpretation of arguments given in command line as an R list of objects
+write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
+
+cat("\n\n")
+
+print("Arguments retrieved from the command line:")
+print(args)
+
+print("Argument types:")
+print(sapply(args, class))
+
+# Check if the image file exists
+if (!file.exists(args$image)) {
+  stop("The RData file does not exist: ", args$image)
+}
+
+# ----- PROCESSING INFILE -----
+
+# Load the RData file
+load(args$image)
+args$image <- NULL
+
+# Save arguments to generate a report
+if (!exists("listOFlistArguments")) listOFlistArguments <- list()
+listOFlistArguments[[format(Sys.time(), "%y%m%d-%H:%M:%S_findIsotopes")]] <- args
+
+# We unzip automatically the chromatograms from the zip files.
+if (!exists("zipfile")) zipfile <- NULL
+if (!exists("singlefile")) singlefile <- NULL
+rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
+zipfile <- rawFilePath$zipfile
+singlefile <- rawFilePath$singlefile
+args <- rawFilePath$args
+
+print(paste("singlefile :", singlefile))
+if (!is.null(singlefile)) {
+  directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
+}
+
+# Verify if the xa object is loaded
+if (!exists("xa")) {
+  stop("The xa object was not found in the RData file.")
+}
+
+print("xa object loaded:")
+print(xa)
+
+print("calcIsotopeMatrix")
+calcIsotopeMatrix <- function(maxiso = 4) {
+  if (!is.numeric(maxiso)) {
+    stop("Parameter maxiso is not numeric!\n")
+  } else if (maxiso < 1 || maxiso > 8) {
+    stop(paste(
+      "Parameter maxiso must be between 1 and 8. ",
+      "Otherwise, use your own IsotopeMatrix.\n"
+    ), sep = "")
+  }
+
+  isotopeMatrix <- matrix(NA, 8, 4)
+  colnames(isotopeMatrix) <- c("mzmin", "mzmax", "intmin", "intmax")
+
+  isotopeMatrix[1, ] <- c(1.000, 1.0040, 1.0, 150)
+  isotopeMatrix[2, ] <- c(0.997, 1.0040, 0.01, 200)
+  isotopeMatrix[3, ] <- c(1.000, 1.0040, 0.001, 200)
+  isotopeMatrix[4, ] <- c(1.000, 1.0040, 0.0001, 200)
+  isotopeMatrix[5, ] <- c(1.000, 1.0040, 0.00001, 200)
+  isotopeMatrix[6, ] <- c(1.000, 1.0040, 0.000001, 200)
+  isotopeMatrix[7, ] <- c(1.000, 1.0040, 0.0000001, 200)
+  isotopeMatrix[8, ] <- c(1.000, 1.0040, 0.00000001, 200)
+
+  return(isotopeMatrix[1:maxiso, , drop = FALSE])
+}
+
+isotopeMatrix <- calcIsotopeMatrix(args$maxiso)
+
+# Apply the findIsotopes function on the xsAnnotate object
+print("Calling findIsotopes function:")
+xa <- findIsotopes(xa, maxcharge = args$maxcharge, maxiso = args$maxiso, ppm = args$ppm, mzabs = args$mzabs, intval = args$intval, minfrac = args$minfrac, isotopeMatrix = isotopeMatrix, filter = args$filter)
+
+print("Result of the findIsotopes function:")
+print(xa)
+
+# Extract the list of annotated peaks
+peakList <- getPeaklist(xa, intval = args$intval)
+
+if (length(phenoData@data$sample_name) == 1) {
+  peakList$name <- make.unique(paste0("M", round(peakList[, "mz"], 0), "T", round(peakList[, "rt"], 0)), "_")
+  variableMetadata <- peakList[, c("name", setdiff(names(peakList), "name"))]
+  variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
+} else {
+  names_default <- groupnames(xa@xcmsSet, mzdec = 0, rtdec = 0) # Names without decimals
+  names_custom <- groupnames(xa@xcmsSet, mzdec = args$numDigitsMZ, rtdec = args$numDigitsRT) # Names with "x" decimals
+
+  variableMetadata <- data.frame(
+    name = names_default,
+    name_custom = names_custom,
+    stringsAsFactors = FALSE
+  )
+  variableMetadata <- cbind(variableMetadata, peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))])
+}
+
+if (!exists("RTinMinute")) RTinMinute <- FALSE
+
+if (args$convertRTMinute && RTinMinute == FALSE) {
+  RTinMinute <- TRUE
+  variableMetadata <- RTSecondToMinute(variableMetadata = variableMetadata, convertRTMinute = args$convertRTMinute)
+}
+
+# Saves the extracted peak list as a TSV file named 'variableMetadata.tsv'
+output_file_tsv <- "variableMetadata.tsv"
+write.table(variableMetadata, file = output_file_tsv, sep = "\t", row.names = FALSE, quote = FALSE)
+
+# Save the updated xsAnnotate object
+output_file_RData <- "camera_findIsotopes.RData"
+
+objects2save <- c("xa", "variableMetadata", "listOFlistArguments", "zipfile", "singlefile", "RTinMinute", "phenoData")
+save(list = objects2save[objects2save %in% ls()], file = output_file_RData)
+
+cat("Output files generated:", output_file_tsv, "and", output_file_RData, "\n")