--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NmrBucketing_wrapper.R	Fri Apr 08 10:56:14 2016 -0400
@@ -0,0 +1,156 @@
+#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
+
+## 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
+
+if(runExampleL) {
+##------------------------------
+## Example of arguments
+##------------------------------
+argLs <- list(StudyDir = "Tlse_BPASourisCerveau",
+              upper = "10.0",
+              lower = "0.50",
+              bucket.width = "0.01",
+              exclusion = "TRUE",
+              exclusion.zone = list(c(6.5,4.5)),
+              graph="Overlay")
+
+argLs <- c(argLs,
+           list(dataMatrixOut = paste(directory,"_NmrBucketing_dataMatrix.tsv",sep=""),
+                sampleMetadataOut = paste(directory,"_NmrBucketing_sampleMetadata.tsv",sep=""),
+                variableMetadataOut = paste(directory,"_NmrBucketing_variableMetadata.tsv",sep=""),
+                graphOut = paste(directory,"_NmrBucketing_graph.pdf",sep=""),
+                logOut = paste(directory,"_NmrBucketing_log.txt",sep="")))
+}
+
+##------------------------------
+## Options
+##------------------------------
+strAsFacL <- options()$stringsAsFactors
+options(stringsAsFactors = FALSE)
+
+
+##------------------------------
+## Libraries laoding
+##------------------------------
+# For parseCommandArgs function
+library(batch) 
+# For cumtrapz function
+library(pracma)
+
+# R script call
+source_local <- function(fname)
+{
+	argv <- commandArgs(trailingOnly = FALSE)
+	base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+	source(paste(base_dir, fname, sep="/"))
+}
+#Import the different functions
+source_local("NmrBucketing_script.R")
+
+##------------------------------
+## Errors ?????????????????????
+##------------------------------
+
+
+##------------------------------
+## Constants
+##------------------------------
+topEnvC <- environment()
+flagC <- "\n"
+
+
+##------------------------------
+## Script
+##------------------------------
+if(!runExampleL)
+    argLs <- parseCommandArgs(evaluate=FALSE)
+
+## sink(argLs[["logOut"]])
+
+
+## Parameters Loading
+##-------------------
+  # Inputs
+if (!is.null(argLs[["zipfile"]])){
+	zipfile= argLs[["zipfile"]]
+	directory=unzip(zipfile, list=F)
+	directory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/")
+} else if (!is.null(argLs[["library"]])){
+	directory=argLs[["library"]]
+    	if(!file.exists(directory)){
+		error_message=paste("Cannot access the directory :",directory,".Please verify if the directory exists or not.")
+		print(error_message)
+		stop(error_message)
+	}
+}
+
+leftBorder <- argLs[["left_border"]]
+rightBorder <- argLs[["right_border"]]
+bucketSize <- argLs[["bucket_width"]]
+exclusionZones <- argLs[["zone_exclusion_choices.choice"]]
+
+exclusionZonesBorders <- NULL
+if (!is.null(argLs$zone_exclusion_left))
+{
+   for(i in which(names(argLs)=="zone_exclusion_left"))
+   {
+     exclusionZonesBorders <- c(exclusionZonesBorders,list(c(argLs[[i]],argLs[[i+1]])))
+   }
+}
+
+graphique <- argLs[["graphType"]]
+
+  # Outputs
+nomGraphe <- argLs[["graphOut"]]
+dataMatrixOut <- argLs[["dataMatrixOut"]]
+sampleMetadataOut <- argLs[["sampleOut"]]
+variableMetadataOut <- argLs[["variableOut"]]
+log <- argLs[["logOut"]]
+
+## Checking arguments
+##-------------------
+error.stock <- "\n"
+
+if(length(error.stock) > 1)
+  stop(error.stock)
+  
+  
+## Computation
+##------------
+outputs <- NmrBucketing(directory,leftBorder,rightBorder,bucketSize,exclusionZones,exclusionZonesBorders,graphique,nomGraphe,log)
+data_bucket <- outputs[[1]]
+data_sample <- outputs[[2]]
+data_variable <- outputs[[3]]
+
+## Saving
+##-------
+  # Data
+data_bucket <- cbind(rownames(data_bucket),data_bucket)
+colnames(data_bucket) <- c("Bucket",colnames(data_bucket)[-1])
+write.table(data_bucket,file=argLs$dataMatrixOut,quote=FALSE,row.names=FALSE,sep="\t")
+  # Sample
+data_sample <- cbind(rownames(data_sample),data_sample)
+colnames(data_sample) <- c("Sample",colnames(data_sample)[-1])
+write.table(data_sample,file=argLs$sampleOut,quote=FALSE,row.names=FALSE,sep="\t")
+  # Variable
+data_variable <- cbind(rownames(data_variable),data_variable)
+colnames(data_variable) <- c("Bucket",colnames(data_variable)[-1])
+write.table(data_variable,file=argLs$variableOut,quote=FALSE,row.names=FALSE,sep="\t")
+
+
+## Ending
+##---------------------
+
+cat("\nEnd of 'NMR bucketing' Galaxy module call: ", as.character(Sys.time()), sep = "")
+
+## sink(NULL)
+
+options(stringsAsFactors = strAsFacL)
+
+rm(list = ls())