comparison xcms_retcor.r @ 50:0bc08f128b42 draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163

49:177b5847a211

# ----- 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("xcms", "batch", "RColorBrewer")
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")

# ----- PROCESSING INFILE -----
cat("\tARGUMENTS PROCESSING INFO\n")

#saving the specific parameters
method <- args$method

cat("\n\n")


# ----- ARGUMENTS PROCESSING -----
cat("\tINFILE PROCESSING INFO\n")

#image is an .RData file necessary to use xset variable given by previous tools
load(args$image)
args$image <- NULL
if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")

# Handle infiles

adjustRtimeParam <- do.call(paste0(method, "Param"), args)
print(adjustRtimeParam)

if (hasAdjustedRtime(xdata)) {
  cat("WARNING: a retention time ajustment had already been applied to your data.\nThe function applyAdjustedRtime was processed to cumulate the ajustment")
  cat("Replace raw retention times with adjusted retention times.\n")
  xdata <- applyAdjustedRtime(xdata)
}
xdata <- adjustRtime(xdata, param = adjustRtimeParam)

cat("\n\n")

# Get the legacy xcmsSet object
xset <- getxcmsSetObject(xdata)
print(xset)
cat("\n\n")

#saving R data in .Rdata file to save the variables used in the present tool
objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
save(list = objects2save[objects2save %in% ls()], file = "retcor.RData")

cat("\n\n")

50:0bc08f128b42

# ----- 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("xcms", "batch", "RColorBrewer")
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")

# ----- PROCESSING INFILE -----
cat("\tARGUMENTS PROCESSING INFO\n")

# saving the specific parameters
method <- args$method

cat("\n\n")


# ----- ARGUMENTS PROCESSING -----
cat("\tINFILE PROCESSING INFO\n")

# image is an .RData file necessary to use xset variable given by previous tools
load(args$image)
args$image <- NULL
if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")

# Handle infiles

adjustRtimeParam <- do.call(paste0(method, "Param"), args)
print(adjustRtimeParam)

if (hasAdjustedRtime(xdata)) {
    cat("WARNING: a retention time ajustment had already been applied to your data.\nThe function applyAdjustedRtime was processed to cumulate the ajustment")
    cat("Replace raw retention times with adjusted retention times.\n")
    xdata <- applyAdjustedRtime(xdata)
}
xdata <- adjustRtime(xdata, param = adjustRtimeParam)

cat("\n\n")

# Get the legacy xcmsSet object
xset <- getxcmsSetObject(xdata)
print(xset)
cat("\n\n")

# saving R data in .Rdata file to save the variables used in the present tool
objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
save(list = objects2save[objects2save %in% ls()], file = "retcor.RData")

cat("\n\n")