--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/profia_wrapper.R	Sun Mar 26 17:37:12 2017 -0400
@@ -0,0 +1,210 @@
+#!/usr/bin/env Rscript
+
+library(batch) ## parseCommandArgs
+
+argVc <- unlist(parseCommandArgs(evaluate=FALSE))
+
+##------------------------------
+## Initializing
+##------------------------------
+
+
+## libraries
+##----------
+
+suppressMessages(library(proFIA))
+
+
+## constants
+##----------
+
+modNamC <- "proFIA" ## module name
+
+
+## log file
+##---------
+
+sink(argVc["information"])
+
+cat("\nStart of the '", modNamC, "' Galaxy module call: ",
+    format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
+
+
+## arguments
+##----------
+
+
+if("zipfile" %in% names(argVc)) {
+    
+    zipfile <- argVc["zipfile"]
+
+    ## We unzip automatically the raw files from the zip file
+    
+    if(exists("zipfile") && (zipfile!="")) {
+        if(!file.exists(zipfile)){
+            error_message=paste("Cannot access the Zip file:", zipfile)
+            print(error_message)
+            stop(error_message)
+        }
+
+        ## unzip
+
+        suppressWarnings(unzip(zipfile, unzip="unzip"))
+        
+        ## get the directory name
+        
+        filesInZip=unzip(zipfile, list=T);
+        directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
+        directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
+        directory = "."
+        if (length(directories) == 1) directory = directories
+        
+        cat("files_root_directory\t",directory,"\n")
+        
+    }
+
+} else if ("library" %in% names(argVc)) {
+
+    directory <- argVc["library"]
+    
+    if(!file.exists(directory)) {
+        
+        error_message=paste("Cannot access the directory:", directory,". Please check that the directory really exists.")
+        print(error_message)
+        stop(error_message)
+        
+    }
+    
+} else {
+
+    error_message <- "No zipfile nor input library available"
+    print(error_message)
+    stop(error_message)
+
+}
+
+##------------------------------
+## Computations
+##------------------------------
+
+
+optWrnN <- options()$warn
+options(warn = -1)
+
+stpI <- 1
+
+cat("\n", stpI, ") Peak detection step ('proFIAset'):\n", sep = "")
+
+fiaset <- proFIAset(directory,
+                    ppm = as.numeric(argVc["ppmN"]),
+                    parallel = FALSE)
+
+stpI <- stpI + 1
+
+cat("\n", stpI, ") Peak alignment ('group.FIA'):\n", sep = "")
+
+fiaset <- group.FIA(fiaset,
+                    ppmGroup = as.numeric(argVc["ppmGroupN"]),
+                    fracGroup = as.numeric(argVc["fracGroupN"]))
+
+stpI <- stpI + 1
+
+cat("\n", stpI, ") Creating the peak table ('makeDataMatrix'):\n", sep = "")
+
+fiaset <- makeDataMatrix(fiaset,
+                         maxo = FALSE)
+
+stpI <- stpI + 1
+
+kI <- as.integer(argVc["kI"])
+
+if(kI > 0) {
+
+    cat("\n", stpI, ") Imputing missing values ('imputeMissingValues.WKNN_TN'):\n", sep = "")
+
+    fiaset <- imputeMissingValues.WKNN_TN(fiaset,
+                                          k = kI)
+
+    stpI <- stpI + 1
+}
+
+options(warn = optWrnN)
+
+
+##------------------------------
+## Ending
+##------------------------------
+
+
+## Plotting
+##---------
+
+cat("\n", stpI, ") Plotting ('plot'):\n", sep = "")
+
+pdf(argVc["figure"])
+
+plot(fiaset)
+
+dev.off()
+
+stpI <- stpI + 1
+
+## Printing
+##---------
+
+cat("\n", stpI, ") Printing ('show'):\n", sep = "")
+
+fiaset
+
+stpI <- stpI + 1
+
+## Exporting
+##----------
+
+cat("\n", stpI, ") Exporting ('exportDataMatrix', 'exportSampleMetadata', 'exportVariableMetadata'):\n", sep = "")
+
+datMN <- exportDataMatrix(fiaset)
+samDF <- exportSampleMetadata(fiaset)
+varDF <- exportVariableMetadata(fiaset)
+
+if(nrow(datMN) == nrow(samDF) && ncol(datMN) == nrow(varDF)) {
+    datDF <- as.data.frame(t(datMN))
+} else {
+    datDF <- as.data.frame(datMN)
+}
+rownames(varDF) <- rownames(datDF)
+
+datDF <- cbind.data.frame(dataMatrix = rownames(datDF),
+                          datDF)
+write.table(datDF,
+            file = argVc["dataMatrix_out"],
+            quote = FALSE,
+            row.names = FALSE,
+            sep = "\t")
+
+samDF <- cbind.data.frame(sampleMetadata = rownames(samDF),
+                          samDF)
+write.table(samDF,
+            file = argVc["sampleMetadata_out"],
+            quote = FALSE,
+            row.names = FALSE,
+            sep = "\t")
+
+varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
+                          varDF)
+write.table(varDF,
+            file = argVc["variableMetadata_out"],
+            quote = FALSE,
+            row.names = FALSE,
+            sep = "\t")
+
+
+## Closing
+##--------
+
+cat("\nEnd of '", modNamC, "' Galaxy module call: ",
+    as.character(Sys.time()), "\n", sep = "")
+
+sink()
+
+rm(list = ls())