--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NmrNormalization_wrapper.R	Tue Oct 02 12:14:47 2018 -0400
@@ -0,0 +1,173 @@
+#!/usr/bin/env Rscript
+
+## 070115_NmrBucketing2galaxy_v1.R
+## Marie Tremblay-Franco
+## MetaboHUB: The French Infrastructure for Metabolomics and Fluxomics
+## www.metabohub.fr/en
+## marie.tremblay-franco@toulouse.inra.fr
+
+runExampleL <- FALSE
+
+
+##------------------------------
+## Options
+##------------------------------
+strAsFacL <- options()$stringsAsFactors
+options(stringsAsFactors = FALSE)
+
+
+##------------------------------
+## Libraries laoding
+##------------------------------
+# For parseCommandArgs function
+library(batch) 
+
+# Constants
+argv <- commandArgs(trailingOnly = FALSE)
+script.path <- sub("--file=","",argv[grep("--file=",argv)])
+prog.name <- basename(script.path)
+
+# Print help
+if (length(grep('-h', argv)) >0) {
+	cat("Usage:", prog.name,
+	    "dataMatrix myDataMatrix.tsv",
+	    "scalingMethod PQN|QuantitativeVariable",
+	    "graphType None|Overlay|One_per_individual",
+	    "logOut myLog.txt",
+	    "dataMatrixOut myDataMatrixOutput.tsv",
+	    "graphOut myGraph.pdf",
+		"\n")
+	quit(status = 0)
+}
+
+# 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("NmrNormalization_script.R")
+source_local("DrawSpec.R")
+
+
+##------------------------------
+## Errors ?????????????????????
+##------------------------------
+
+
+##------------------------------
+## Constants
+##------------------------------
+topEnvC <- environment()
+flagC <- "\n"
+
+
+##------------------------------
+## Script
+##------------------------------
+if(!runExampleL)
+    argLs <- parseCommandArgs(evaluate=FALSE)
+
+
+## Parameters Loading
+##-------------------
+  # Inputs
+data <- read.table(argLs[["dataMatrix"]], check.names=FALSE, header=TRUE, sep="\t", row.names=1)
+names <- rownames(data)
+	## Add a test to check if all values are numercical
+if (!all(vapply(data, is.numeric, FUN.VALUE = FALSE)))
+  stop("Data are not numeric")
+	## Integer conversion to avoid stack overflow when computin the sum
+data <- as.data.frame(lapply(data, as.numeric))
+rownames(data) <- names
+
+scaling <- argLs[["scalingMethod"]]
+graphique <- argLs[["graphType"]]
+
+if (scaling=='PQN')
+{
+ metadataSample <- read.table(argLs[["sampleMetadata"]],check.names=FALSE,header=TRUE,sep="\t")
+ factor<- argLs[["factor"]]
+ ControlGroup <- argLs[["controlGroup"]]
+}
+if (scaling=='QuantitativeVariable')
+{
+  metadataSample <- read.table(argLs[["sampleMetadata"]],check.names=FALSE,header=TRUE,sep="\t")
+  factor <- argLs[["factor"]]
+}
+
+  # Outputs
+nomGraphe <- argLs[["graphOut"]]
+dataMatrixOut <- argLs[["dataMatrixOut"]]
+log <- argLs[["logOut"]]
+
+
+## Checking R packages
+##--------------------
+sink(log)
+cat("\tPACKAGE INFO\n")
+pkgs=c("batch")
+for(pkg in pkgs) {
+    suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
+    cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
+}
+cat("\n")
+
+
+## Checking arguments
+##-------------------
+error.stock <- "\n"
+if(length(error.stock) > 1)
+  stop(error.stock)
+  
+  
+## Computation
+##------------
+NormalizationResults <- NmrNormalization(dataMatrix=data,scalingMethod=scaling,sampleMetadata=metadataSample,
+                                    bioFactor=factor,ControlGroup=ControlGroup,
+                                    graph=graphique,nomFichier=nomGraphe,savLog.txtC=log)
+
+data_normalized <- NormalizationResults[[1]]
+
+
+## Graphical outputs
+##------------------
+if (graphique != "None")
+{
+  # Graphic Device opening
+  pdf(nomGraphe,onefile=TRUE)
+  
+  if (graphique == "Overlay")
+  {
+    # Global spectral window
+    spectra <- data.frame(t(data_normalized))
+    drawSpec(spectra,xlab="", ylab="Intensity", main="")
+  }
+  else
+  {
+    for (i in 1:ncol(data_normalized))
+    {
+      spectra <- t(data_normalized[,i])
+      drawSpec(spectra,xlab="", ylab="Intensity", main=colnames(data_normalized)[i])
+    }
+  }
+  dev.off()
+}
+
+
+## Saving
+##-------
+  # Data
+data_normalized <- cbind(rownames(data_normalized),data_normalized)
+colnames(data_normalized) <- c("Variable",colnames(data_normalized)[-1])
+write.table(data_normalized,file=argLs$dataMatrixOut,quote=FALSE,row.names=FALSE,sep="\t")
+
+
+## Ending
+##---------------------
+cat("\nEnd of 'Normalization' Galaxy module call: ", as.character(Sys.time()), sep = "")
+sink()
+options(stringsAsFactors = strAsFacL)
+rm(list = ls())