annotate CAMERA_findIsotopes.R @ 0:a8aa53d54c88 draft default tip

planemo upload commit 24d44ee26b7c23380c2b42fae2f7f6e58472100d

#!/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")