--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nmr_preprocessing/NmrPreprocessing_wrapper.R	Fri May 05 07:13:02 2017 -0400
@@ -0,0 +1,320 @@
+#!/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)
+
+
+# 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="/"))
+}
+#Import the different functions
+source_local("NmrPreprocessing_script.R")
+source_local("DrawFunctions.R")
+
+##------------------------------
+## Errors ?????????????????????
+##------------------------------
+
+
+##------------------------------
+## Constants
+##------------------------------
+topEnvC <- environment()
+flagC <- "\n"
+
+
+##------------------------------
+## Script
+##------------------------------
+if(!runExampleL)
+    argLs <- parseCommandArgs(evaluate=FALSE)
+
+# log file
+print(argLs[["logOut"]])
+
+## Starting
+cat("\nStart of 'Preprocessing' Galaxy module call: ", as.character(Sys.time()), sep = "")
+
+
+##======================================================
+##======================================================
+## Parameters Loading
+##======================================================
+##======================================================
+
+# 1rst order phase correction ------------------------
+  # 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")
+samplemetadataFid <- as.matrix(samplemetadataFid)
+
+
+# water and solvent(s) correction ------------------------
+  # Inputs
+lambda <- argLs[["lambda"]]
+ptwSS1 <- argLs[["ptwSS"]]
+ptwSS <- FALSE
+if (ptwSS1=="YES")
+ 	ptwSS <- TRUE
+
+
+# apodization -----------------------------------------
+  # 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"]]
+  }		
+
+
+# Fourier transform ----------------------------------
+  # Inputs
+FTGraph <- argLs[["FTGraph"]]
+
+# Internal referencering ----------------------------------
+  # Inputs
+shiftTreshold = 2 # c
+ppm = TRUE
+shiftReferencingRangeList = NULL  # fromto.RC
+pctNear0 = 0.02 # pc 
+rowindex_graph = NULL
+ppm_ref = 0 # ppm.ref
+
+# 
+# shiftReferencing <- argLs[["shiftReferencing"]]
+# print(shiftReferencing)
+# 
+# if (shiftReferencing=="YES")
+# {
+#   
+	shiftReferencingMethod <- argLs[["shiftReferencingMethod"]]
+
+	if (shiftReferencingMethod == "thres")	{
+		shiftTreshold <- argLs[["shiftTreshold"]]
+	}
+	
+	shiftReferencingRange <- argLs[["shiftReferencingRange"]]
+	
+	if (shiftReferencingRange == "near0"){
+	  pctNear0 <- argLs[["pctNear0"]]
+	}
+	
+	if (shiftReferencingRange == "window"){
+	  shiftReferencingRangeList <- NULL
+		shiftReferencingRangeLeft <- argLs[["shiftReferencingRangeLeft"]]
+		shiftReferencingRangeRight <- argLs[["shiftReferencingRangeRight"]]
+		shiftReferencingRangeList <- list(shiftReferencingRangeList,c(shiftReferencingRangeLeft,shiftReferencingRangeRight))
+	}
+	
+	shiftHandling <- argLs[["shiftHandling"]]
+	
+	ppm_ref <-  argLs[["ppm_ref"]]
+	
+# }
+
+
+# Zero Order Phase Correction -------------------------------
+  # Inputs
+plot_rms = NULL
+returnAngle = FALSE
+createWindow = TRUE
+angle = NULL
+plot_spectra = FALSE
+quant = 0.95
+ppm = TRUE
+fromto.0OPC = NULL
+zeroOrderPhaseMethod <- argLs[["zeroOrderPhaseMethod"]]
+if (zeroOrderPhaseMethod=='rms')
+{
+  quant <- argLs[["quant"]]
+}
+if (zeroOrderPhaseMethod=='max')
+{
+  angle <- argLs[["angle"]]
+}
+
+searchZoneZeroPhase <- argLs[["searchZoneZeroPhase.choice"]]
+if (searchZoneZeroPhase == "YES") {
+  searchZoneZeroPhaseList <- NULL
+  searchZoneZeroPhaseLeft <- argLs[["shiftReferencingRangeLeft"]]
+  searchZoneZeroPhaseRight <- argLs[["shiftReferencingRangeRight"]]
+  searchZoneZeroPhaseList <- list(searchZoneZeroPhaseList,c(searchZoneZeroPhaseLeft,searchZoneZeroPhaseRight))
+  }
+
+
+
+# Baseline Correction -------------------------------
+  # Inputs
+ptwBc <- as.logical(argLs[["ptwBc"]])
+maxIter <- argLs[["maxIter"]] 
+lambdaBc <- argLs[["lambdaBc"]] 
+pBc <- argLs[["pBc"]] 
+epsilon <- argLs[["epsilon"]] 
+
+
+
+# transformation of negative values -------------------------------
+  # Inputs
+NegativetoZero <- argLs[["NegativetoZero"]]
+
+
+  # Outputs
+nomGraphe <- argLs[["graphOut"]]
+dataMatrixOut <- argLs[["dataMatrixOut"]]
+log <- argLs[["logOut"]]
+
+
+
+## Checking arguments
+##-------------------
+error.stock <- "\n"
+
+if(length(error.stock) > 1)
+  stop(error.stock)
+  
+
+##======================================================
+##======================================================  
+## Computation
+##======================================================
+##======================================================
+
+pdf(nomGraphe, onefile = TRUE, width = 13, height = 13)
+
+# FirstOrderPhaseCorrection ---------------------------------
+Fid_data <- FirstOrderPhaseCorrection(Fid_data0, Fid_info = samplemetadataFid, group_delay = NULL)
+
+
+# SolventSuppression ---------------------------------
+Fid_data <- SolventSuppression(Fid_data, lambda.ss = lambda, ptw.ss = ptwSS, plotSolvent = F, returnSolvent = 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)
+
+# FourierTransform ---------------------------------
+Spectrum_data <- FourierTransform(Fid_data, Fid_info = samplemetadataFid, reverse.axis = TRUE)
+
+
+if (FTGraph == "YES") {
+  title = "Fourier transformed specta"
+  DrawSignal(Spectrum_data, subtype = "stacked",
+             ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T, 
+             xlab = "Frequency", num.stacked = 4, 
+             main = title, createWindow=FALSE)
+}
+
+# InternalReferencing ---------------------------------
+# if (shiftReferencing=="YES") {
+Spectrum_data <- InternalReferencing(Spectrum_data, samplemetadataFid, method = shiftReferencingMethod, range = shiftReferencingRange, 
+                                     ppm.ref = 0, shiftHandling = shiftHandling,ppm = TRUE,
+											 c = shiftTreshold, fromto.RC = shiftReferencingRangeList, pc = pctNear0)
+
+# }
+
+# ZeroOrderPhaseCorrection ---------------------------------
+Spectrum_data  <- ZeroOrderPhaseCorrection(Spectrum_data, method = zeroOrderPhaseMethod, 
+                                           plot_rms = plot_rms, returnAngle = returnAngle, 
+                                           createWindow = createWindow,angle = angle, 
+                                           plot_spectra = plot_spectra, quant = quant, 
+                                           ppm = ppm, fromto.0OPC = fromto.0OPC)
+
+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, maxIter = maxIter, lambda.bc = lambdaBc, p.bc = pBc, eps = epsilon, returnBaseline = F) 
+
+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)
+
+  title = "Spectra after Negative Values Zeroing"
+  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())
+
+##======================================================
+##======================================================
+## Saving
+##======================================================
+##======================================================
+
+# Data Matrix
+write.table(t(Re(Spectrum_data)),file=argLs$dataMatrixOut, quote=FALSE, row.names=TRUE, sep="\t", col.names=TRUE)
+
+
+## Ending
+
+cat("\nEnd of 'Preprocessing' Galaxy module call: ", as.character(Sys.time()), sep = "")
+
+sink()
+
+options(stringsAsFactors = strAsFacL)
+
+rm(list = ls())