diff NmrPreprocessing_wrapper.R @ 7:122df1bf0a8c draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995

--- a/NmrPreprocessing_wrapper.R	Wed May 13 03:52:09 2020 -0400
+++ b/NmrPreprocessing_wrapper.R	Fri Jul 11 08:33:38 2025 +0000
@@ -1,83 +1,60 @@
-#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
-
-## 170116_NmrPreprocessing.R
-## Manon Martin and Marie Tremblay-Franco
-
-##======================================================
-##======================================================
-# Preamble
-##======================================================
-##======================================================
-
-runExampleL <- FALSE
-
-
-##------------------------------
-## Options
-##------------------------------
-strAsFacL <- options()$stringsAsFactors
-options(stringsAsFactors = FALSE)
-
-##------------------------------
 ## Libraries laoding
-##------------------------------
-library(batch)
+## ------------------------------
 library(ptw)
 library(Matrix)
 library(ggplot2)
 library(gridExtra)
 library(reshape2)
 
+# In-house function for argument parsing
+parse_args <- function() {
+    args <- commandArgs()
+    start <- which(args == "--args")[1] + 1
+    if (is.na(start)) {
+        return(list())
+    }
+    seq_by2 <- seq(start, length(args), by = 2)
+    result <- as.list(args[seq_by2 + 1])
+    names(result) <- args[seq_by2]
+    return(result)
+}
 
 # R script call
-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 <- function(fname) {
+    argv <- commandArgs(trailingOnly = FALSE)
+    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+    source(paste(base_dir, fname, sep = "/"))
 }
-#Import the different functions
+# Import the different functions
 source_local("NmrPreprocessing_script.R")
 source_local("DrawFunctions.R")
 
-##------------------------------
+## ------------------------------
 ## Script
-##------------------------------
+## ------------------------------
 runExampleL <- FALSE
 
-
-if(!runExampleL)
-  argLs <- parseCommandArgs(evaluate=FALSE)
-
-sink(argLs$logOut)
-
+if (!runExampleL) {
+    argLs <- unlist(parse_args())
+}
+# input arguments
+cat("\n INPUT and OUTPUT ARGUMENTS :\n")
+print(argLs)
 
-##------------------------------
-## Errors ?????????????????????
-##------------------------------
-
-
-##------------------------------
+## ------------------------------
 ## Constants
-##------------------------------
+## ------------------------------
 topEnvC <- environment()
 flagC <- "\n"
 
-
-
-
-# log file
-# print(argLs[["logOut"]])
-
 ## Starting
 cat("\nStart of 'Preprocessing' Galaxy module call: ", as.character(Sys.time()), "\n", sep = "")
 
-
-##======================================================
-##======================================================
+## ======================================================
+## ======================================================
 ## Parameters Loading
-##======================================================
-##======================================================
+## ======================================================
+## ======================================================
 
 # graphical inputs
 FirstOPCGraph <- argLs[["FirstOPCGraph"]]
@@ -89,208 +66,191 @@
 BCGraph <- argLs[["BCGraph"]]
 FinalGraph <- argLs[["FinalGraph"]]
 
-
 # 1rst order phase correction ------------------------
-  # Inputs
-	## Data matrix
-Fid_data0 <- read.table(argLs[["dataMatrixFid"]],header=TRUE, check.names=FALSE, sep='\t')
+# Inputs
+## Data matrix
+Fid_data0 <- read.table(argLs[["dataMatrixFid"]], header = TRUE, check.names = FALSE, sep = "\t")
 # Fid_data0 <- Fid_data0[,-1]
 Fid_data0 <- as.matrix(Fid_data0)
 
-	## Samplemetadata
-samplemetadataFid <- read.table(argLs[["sampleMetadataFid"]],check.names=FALSE,header=TRUE,sep="\t")
+## Samplemetadata
+samplemetadataFid <- read.table(argLs[["sampleMetadataFid"]], check.names = FALSE, header = TRUE, sep = "\t")
 samplemetadataFid <- as.matrix(samplemetadataFid)
 
-
 # water and solvent(s) correction ------------------------
-  # Inputs
-lambda <- argLs[["lambda"]]
-
-
+# Inputs
+lambda <- as.numeric(argLs[["lambda"]])
 
 # apodization -----------------------------------------
-  # Inputs
-phase=0
-rectRatio=1/2
-gaussLB=1
-expLB=1
+# Inputs
+phase <- 0
+rectRatio <- 1 / 2
+gaussLB <- 1
+expLB <- 1
 apodization <- argLs[["apodizationMethod"]]
 
-if (apodization=='exp'){
-  expLB <- argLs[["expLB"]]
-  } else if (apodization=='cos2'){
-  phase <- argLs[["phase"]]
-  } else if (apodization=='hanning'){
-  phase <- argLs[["phase"]]
-  } else if (apodization=='hamming'){
-  phase <- argLs[["phase"]]
-  } else if (apodization=='blockexp'){
-  rectRatio <- argLs[["rectRatio"]]
-  expLB <- argLs[["expLB"]]
-  } else if (apodization=='blockcos2'){
-  rectRatio <- argLs[["rectRatio"]]
-  } else if (apodization=='gauss'){
-  rectRatio <- argLs[["rectRatio"]]
-  gaussLB <- argLs[["gaussLB"]]
-  }		
-
+if (apodization == "exp") {
+    expLB <- as.numeric(argLs[["expLB"]])
+} else if (apodization == "cos2") {
+    phase <- as.numeric(argLs[["phase"]])
+} else if (apodization == "hanning") {
+    phase <- as.numeric(argLs[["phase"]])
+} else if (apodization == "hamming") {
+    phase <- as.numeric(argLs[["phase"]])
+} else if (apodization == "blockexp") {
+    rectRatio <- as.numeric(argLs[["rectRatio"]])
+    expLB <- as.numeric(argLs[["expLB"]])
+} else if (apodization == "blockcos2") {
+    rectRatio <- as.numeric(argLs[["rectRatio"]])
+} else if (apodization == "gauss") {
+    rectRatio <- as.numeric(argLs[["rectRatio"]])
+    gaussLB <- as.numeric(argLs[["gaussLB"]])
+}
 
 # Fourier transform ----------------------------------
-  # Inputs
-
+# Inputs
 
 # Zero Order Phase Correction -------------------------------
-  # Inputs
-
-angle = NULL
-excludeZOPC = NULL
-
+# Inputs
+angle <- NULL
+excludeZOPC <- NULL
 
 zeroOrderPhaseMethod <- argLs[["zeroOrderPhaseMethod"]]
-										   
-if (zeroOrderPhaseMethod=='manual'){
-  angle <- argLs[["angle"]]
+
+if (zeroOrderPhaseMethod == "manual") {
+    angle <- argLs[["angle"]]
 }
 
 excludeZoneZeroPhase <- argLs[["excludeZoneZeroPhase.choice"]]
-if (excludeZoneZeroPhase == 'YES') {
-  excludeZoneZeroPhaseList <- list()
-  for(i in which(names(argLs)=="excludeZoneZeroPhase_left")) {
-    excludeZoneZeroPhaseLeft <- argLs[[i]]
-    excludeZoneZeroPhaseRight <- argLs[[i+1]]
-    excludeZoneZeroPhaseList <- c(excludeZoneZeroPhaseList,list(c(excludeZoneZeroPhaseLeft,excludeZoneZeroPhaseRight)))
-  }
-  excludeZOPC <- excludeZoneZeroPhaseList
+if (excludeZoneZeroPhase == "YES") {
+    excludeZoneZeroPhaseList <- list()
+    for (i in which(names(argLs) == "excludeZoneZeroPhase_left")) {
+        excludeZoneZeroPhaseLeft <- as.numeric(argLs[[i]])
+        excludeZoneZeroPhaseRight <- as.numeric(argLs[[i + 1]])
+        excludeZoneZeroPhaseList <- c(excludeZoneZeroPhaseList, list(c(excludeZoneZeroPhaseLeft, excludeZoneZeroPhaseRight)))
+    }
+    excludeZOPC <- excludeZoneZeroPhaseList
 }
 
-
 # Internal referencering ----------------------------------
 # Inputs
-shiftTreshold = 2 # c
-ppm = TRUE
-shiftReferencingRangeList = NULL  # fromto.RC
-pctNearValue = 0.02 # pc 
-rowindex_graph = NULL
-ppm_ref = 0 # ppm.ref
+shiftTreshold <- 2
+ppm <- TRUE
+shiftReferencingRangeList <- NULL # fromto.RC
+pctNearValue <- 0.02 # pc
+rowindex_graph <- NULL
+ppm_ref <- 0 # ppm.ref
 
-# 
 # shiftReferencing <- argLs[["shiftReferencing"]]
 # print(shiftReferencing)
-# 
-# if (shiftReferencing=="YES")
-# {
-#   
+#
+# if (shiftReferencing=="YES") {
+#
 # shiftReferencingMethod <- argLs[["shiftReferencingMethod"]]
-# 
+#
 # if (shiftReferencingMethod == "thres")	{
 # 	shiftTreshold <- argLs[["shiftTreshold"]]
 # }
 
 shiftReferencingRange <- argLs[["shiftReferencingRange"]]
-
-if (shiftReferencingRange == "near0"){
-  pctNearValue <- argLs[["pctNearValue"]]
+if (shiftReferencingRange == "near0") {
+    pctNearValue <- as.numeric(argLs[["pctNearValue"]])
 }
 
-if (shiftReferencingRange == "window"){
-  shiftReferencingRangeList <- list()
-  for(i in which(names(argLs)=="shiftReferencingRangeLeft")) 
-  {
-    shiftReferencingRangeLeft <- argLs[[i]]
-    shiftReferencingRangeRight <- argLs[[i+1]]
-    shiftReferencingRangeList <- c(shiftReferencingRangeList,list(c(shiftReferencingRangeLeft,shiftReferencingRangeRight)))
-  }
+if (shiftReferencingRange == "window") {
+    shiftReferencingRangeList <- list()
+    for (i in which(names(argLs) == "shiftReferencingRangeLeft"))
+    {
+        shiftReferencingRangeLeft <- as.numeric(argLs[[i]])
+        shiftReferencingRangeRight <- as.numeric(argLs[[i + 1]])
+        shiftReferencingRangeList <- c(shiftReferencingRangeList, list(c(shiftReferencingRangeLeft, shiftReferencingRangeRight)))
+    }
 }
-
 shiftHandling <- argLs[["shiftHandling"]]
 
-ppmvalue <- argLs[["ppmvalue"]]
-
-
-
+ppmvalue <- as.numeric(argLs[["ppmvalue"]])
 # }
 
-
 # Baseline Correction -------------------------------
-  # Inputs
-lambdaBc <- argLs[["lambdaBc"]] 
-pBc <- argLs[["pBc"]] 
-epsilon <- argLs[["epsilon"]] 
+# Inputs
+lambdaBc <- as.numeric(argLs[["lambdaBc"]])
+pBc <- as.numeric(argLs[["pBc"]])
+epsilon <- as.numeric(argLs[["epsilon"]])
 
-excludeBC = NULL
+excludeBC <- NULL
 
 excludeZoneBC <- argLs[["excludeZoneBC.choice"]]
-if (excludeZoneBC == 'YES') {
-  excludeZoneBCList <- list()
-  for(i in which(names(argLs)=="excludeZoneBC_left")) {
-    excludeZoneBCLeft <- argLs[[i]]
-    excludeZoneBCRight <- argLs[[i+1]]
-    excludeZoneBCList <- c(excludeZoneBCList,list(c(excludeZoneBCLeft,excludeZoneBCRight)))
-  }
-  excludeBC <- excludeZoneBCList
+if (excludeZoneBC == "YES") {
+    excludeZoneBCList <- list()
+    for (i in which(names(argLs) == "excludeZoneBC_left")) {
+        excludeZoneBCLeft <- as.numeric(argLs[[i]])
+        excludeZoneBCRight <- as.numeric(argLs[[i + 1]])
+        excludeZoneBCList <- c(excludeZoneBCList, list(c(excludeZoneBCLeft, excludeZoneBCRight)))
+    }
+    excludeBC <- excludeZoneBCList
 }
 
 # transformation of negative values -------------------------------
-  # Inputs
+# Inputs
 NegativetoZero <- argLs[["NegativetoZero"]]
 
-
-  # Outputs
+# Outputs
 nomGraphe <- argLs[["graphOut"]]
-# dataMatrixOut <- argLs[["dataMatrixOut"]]
 log <- argLs[["logOut"]]
 
-
-
 ## Checking arguments
-##-------------------
+## -------------------
 error.stock <- "\n"
-
-if(length(error.stock) > 1)
-  stop(error.stock)
-  
+if (length(error.stock) > 1) {
+    stop(error.stock)
+}
 
-##======================================================
-##======================================================  
+## ======================================================
 ## Computation
-##======================================================
-##======================================================
-
+## ======================================================
 pdf(nomGraphe, onefile = TRUE, width = 13, height = 13)
 
 # FirstOrderPhaseCorrection ---------------------------------
 Fid_data <- GroupDelayCorrection(Fid_data0, Fid_info = samplemetadataFid, group_delay = NULL)
 
 if (FirstOPCGraph == "YES") {
-  title = "FIDs after Group Delay Correction"
-  DrawSignal(Fid_data, subtype = "stacked",
-             ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, 
-             xlab = "Frequency", num.stacked = 4, 
-             main = title, createWindow=FALSE)
+    title <- "FIDs after Group Delay Correction"
+    DrawSignal(Fid_data,
+        subtype = "stacked",
+        ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T,
+        xlab = "Frequency", num.stacked = 4,
+        main = title, createWindow = FALSE
+    )
 }
 
 # SolventSuppression ---------------------------------
 Fid_data <- SolventSuppression(Fid_data, lambda.ss = lambda, ptw.ss = TRUE, plotSolvent = F, returnSolvent = F)
-	
+
 if (SSGraph == "YES") {
-  title = "FIDs after Solvent Suppression "
-  DrawSignal(Fid_data, subtype = "stacked",
-             ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, 
-             xlab = "Frequency", num.stacked = 4, 
-             main = title, createWindow=FALSE)
+    title <- "FIDs after Solvent Suppression "
+    DrawSignal(Fid_data,
+        subtype = "stacked",
+        ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T,
+        xlab = "Frequency", num.stacked = 4,
+        main = title, createWindow = FALSE
+    )
 }
 
 
-# Apodization ---------------------------------	
-Fid_data <- Apodization(Fid_data, Fid_info = samplemetadataFid, DT = NULL, 
-                         type.apod = apodization, phase = phase, rectRatio = rectRatio, gaussLB = gaussLB, expLB = expLB, plotWindow = F, returnFactor = F)
+# Apodization ---------------------------------
+Fid_data <- Apodization(Fid_data,
+    Fid_info = samplemetadataFid, DT = NULL,
+    type.apod = apodization, phase = phase, rectRatio = rectRatio, gaussLB = gaussLB, expLB = expLB, plotWindow = F, returnFactor = F
+)
 
 if (ApodGraph == "YES") {
-  title = "FIDs after Apodization"
-  DrawSignal(Fid_data, subtype = "stacked",
-             ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, 
-             xlab = "Frequency", num.stacked = 4, 
-             main = title, createWindow=FALSE)
+    title <- "FIDs after Apodization"
+    DrawSignal(Fid_data,
+        subtype = "stacked",
+        ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T,
+        xlab = "Frequency", num.stacked = 4,
+        main = title, createWindow = FALSE
+    )
 }
 
 
@@ -299,113 +259,137 @@
 
 
 if (FTGraph == "YES") {
-  title = "Fourier transformed spectra"
-  DrawSignal(Spectrum_data, subtype = "stacked",
-             ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, 
-             xlab = "Frequency", num.stacked = 4, 
-             main = title, createWindow=FALSE)
+    title <- "Fourier transformed spectra"
+    DrawSignal(Spectrum_data,
+        subtype = "stacked",
+        ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T,
+        xlab = "Frequency", num.stacked = 4,
+        main = title, createWindow = FALSE
+    )
 }
 
 
+# if (FTGraph == "YES") {
+#   title = "Fourier transformed spectra"
+# DrawSignal(Spectrum_data, subtype = "stacked",
+#            ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T,
+#            xlab = "Frequency", num.stacked = 4,
+#            main = title, createWindow=FALSE)
+# }
 
 # ZeroOrderPhaseCorrection ---------------------------------
-Spectrum_data  <- ZeroOrderPhaseCorrection(Spectrum_data, type.zopc = zeroOrderPhaseMethod,
-                                           plot_rms = NULL, returnAngle = FALSE,
-                                           createWindow = TRUE,angle = angle,
-                                           plot_spectra = FALSE,
-                                           ppm.zopc = TRUE, exclude.zopc = excludeZOPC)
+Spectrum_data <- ZeroOrderPhaseCorrection(Spectrum_data,
+    type.zopc = zeroOrderPhaseMethod,
+    plot_rms = NULL, returnAngle = FALSE,
+    createWindow = TRUE, angle = angle,
+    plot_spectra = FALSE,
+    ppm.zopc = TRUE, exclude.zopc = excludeZOPC
+)
 
 
 # InternalReferencing ---------------------------------
 # if (shiftReferencing=="YES") {
-Spectrum_data <- InternalReferencing(Spectrum_data, samplemetadataFid, method = "max", range = shiftReferencingRange,
-                                     ppm.value = ppmvalue, shiftHandling = shiftHandling, ppm.ir = TRUE,
-                                     fromto.RC = shiftReferencingRangeList, pc = pctNearValue)
+Spectrum_data <- InternalReferencing(Spectrum_data, samplemetadataFid,
+    method = "max", range = shiftReferencingRange,
+    ppm.value = ppmvalue, shiftHandling = shiftHandling, ppm.ir = TRUE,
+    fromto.RC = shiftReferencingRangeList, pc = pctNearValue
+)
 
 if (SRGraph == "YES") {
-  title = "Spectra after Shift Referencing"
-  DrawSignal(Spectrum_data, subtype = "stacked",
-             ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, 
-             xlab = "Frequency", num.stacked = 4, 
-             main = title, createWindow=FALSE)
+    title <- "Spectra after Shift Referencing"
+    DrawSignal(Spectrum_data,
+        subtype = "stacked",
+        ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T,
+        xlab = "Frequency", num.stacked = 4,
+        main = title, createWindow = FALSE
+    )
 }
 
 # }
 
 if (ZeroOPCGraph == "YES") {
-title = "Spectra after Zero Order Phase Correction"
-DrawSignal(Spectrum_data, subtype = "stacked",
-           ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, 
-           xlab = "Frequency", num.stacked = 4, 
-           main = title, createWindow=FALSE)
+    title <- "Spectra after Zero Order Phase Correction"
+    DrawSignal(Spectrum_data,
+        subtype = "stacked",
+        ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T,
+        xlab = "Frequency", num.stacked = 4,
+        main = title, createWindow = FALSE
+    )
 }
 
 
-# BaselineCorrection ---------------------------------									 
-Spectrum_data <- BaselineCorrection(Spectrum_data, ptw.bc = TRUE, lambda.bc = lambdaBc, 
-                                    p.bc = pBc, eps = epsilon, ppm.bc = TRUE, 
-                                    exclude.bc = excludeBC,
-                                    returnBaseline = F) 
+# BaselineCorrection ---------------------------------
+Spectrum_data <- BaselineCorrection(Spectrum_data,
+    ptw.bc = TRUE, lambda.bc = lambdaBc,
+    p.bc = pBc, eps = epsilon, ppm.bc = TRUE,
+    exclude.bc = excludeBC,
+    returnBaseline = F
+)
 
 
 
 if (BCGraph == "YES") {
-title = "Spectra after Baseline Correction"
-DrawSignal(Spectrum_data, subtype = "stacked",
-           ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, 
-           xlab = "Frequency", num.stacked = 4, 
-           main = title, createWindow=FALSE)
-}
-
-
-# NegativeValuesZeroing ---------------------------------
-if (NegativetoZero=="YES") {
-  Spectrum_data <- NegativeValuesZeroing(Spectrum_data)
-}
-
-if (FinalGraph == "YES") {
-  title = "Final preprocessed spectra"
-  DrawSignal(Spectrum_data, subtype = "stacked",
-             ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, 
-             xlab = "Frequency", num.stacked = 4, 
-             main = title, createWindow=FALSE)
+    title <- "Spectra after Baseline Correction"
+    DrawSignal(Spectrum_data,
+        subtype = "stacked",
+        ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T,
+        xlab = "Frequency", num.stacked = 4,
+        main = title, createWindow = FALSE
+    )
 }
 
+# if (BCGraph == "YES") {
+# title = "Spectra after Baseline Correction"
+# DrawSignal(Spectrum_data, subtype = "stacked",
+#          ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T,
+#          xlab = "Frequency", num.stacked = 4,
+#          main = title, createWindow=FALSE)
+# }
+
+# NegativeValuesZeroing ---------------------------------
+if (NegativetoZero == "YES") {
+    Spectrum_data <- NegativeValuesZeroing(Spectrum_data)
+}
+print(Spectrum_data[1:5, 1:5])
+if (FinalGraph == "YES") {
+    title <- "Final preprocessed spectra"
+    DrawSignal(Spectrum_data,
+        subtype = "stacked",
+        ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T,
+        xlab = "Frequency", num.stacked = 4,
+        main = title, createWindow = FALSE
+    )
+}
 invisible(dev.off())
 
+# data_variable <- matrix(NA, nrow = 1, ncol = dim(Spectrum_data)[2], dimnames = list("ID", NULL))
+# colnames(data_variable) <- colnames(Spectrum_data)
+# data_variable[1,] <- colnames(data_variable)
 
-data_variable <- matrix(NA, nrow = 1, ncol = dim(Spectrum_data)[2], dimnames = list("ID", NULL)) 
+data_variable <- matrix(NA, nrow = 1, ncol = dim(Spectrum_data)[2], dimnames = list("ID", NULL))
 colnames(data_variable) <- colnames(Spectrum_data)
-data_variable[1,] <- colnames(data_variable)
+data_variable[1, ] <- colnames(data_variable)
 
 
-##======================================================
-##======================================================
+## ======================================================
+## ======================================================
 ## Saving
-##======================================================
-##======================================================
+## ======================================================
+## ======================================================
 
 # Data Matrix
-write.table(round(t(Re(Spectrum_data)),6), file=argLs$dataMatrix, quote=FALSE, row.names=TRUE, sep="\t", col.names=TRUE)
+write.table(round(t(Re(Spectrum_data)), 6), file = argLs[["dataMatrix"]], quote = FALSE, row.names = TRUE, sep = "\t", col.names = TRUE)
 
 # Variable metadata
-write.table(data_variable,file=argLs$variableMetadata, quote=FALSE, row.names=TRUE, sep="\t", col.names=TRUE)
-
-# log file
-# write.table(t(data.frame(argLs)), file = argLs$logOut, col.names = FALSE, quote=FALSE)
+write.table(data_variable, file = argLs[["variableMetadata"]], quote = FALSE, row.names = TRUE, sep = "\t", col.names = TRUE)
 
 # input arguments
 cat("\n INPUT and OUTPUT ARGUMENTS :\n")
-
 argLs
 
-
 ## Ending
-
+cat("\nVersion of R librairies")
+print(sessionInfo())
 cat("\nEnd of 'Preprocessing' Galaxy module call: ", as.character(Sys.time()), sep = "")
 
-sink()
-
-options(stringsAsFactors = strAsFacL)
-
 rm(list = ls())