diff NmrBucketing_wrapper.R @ 4:d61f6ceef5d6 draft

planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit a0155b12acca444f72ff761fcce740e71be28a6d-dirty

--- a/NmrBucketing_wrapper.R	Fri Aug 12 05:47:27 2016 -0400
+++ b/NmrBucketing_wrapper.R	Tue Nov 22 05:22:03 2016 -0500
@@ -77,18 +77,23 @@
 ## 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)
-	}
-}
+if (!is.null(argLs[["zipfile"]])){
+	fileType="zip"
+	zipfile= argLs[["zipfile"]]
+	directory=unzip(zipfile, list=F)
+	directory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/")
+} else if (!is.null(argLs[["library"]])){
+	fileType="zip"
+	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)
+	}
+} else if (!is.null(argLs[["tsvfile"]])){
+	fileType="tsv"
+	directory <- read.table(argLs[["tsvfile"]],check.names=FALSE,header=TRUE,sep="\t")
+}
 
 leftBorder <- argLs[["left_border"]]
 rightBorder <- argLs[["right_border"]]
@@ -111,7 +116,7 @@
 dataMatrixOut <- argLs[["dataMatrixOut"]]
 sampleMetadataOut <- argLs[["sampleOut"]]
 variableMetadataOut <- argLs[["variableOut"]]
-log <- argLs[["logOut"]]
+logFile <- argLs[["logOut"]]
 
 ## Checking arguments
 ##-------------------
@@ -123,7 +128,9 @@
   
 ## Computation
 ##------------
-outputs <- NmrBucketing(directory,leftBorder,rightBorder,bucketSize,exclusionZones,exclusionZonesBorders,graphique,nomGraphe,log)
+outputs <- NmrBucketing(fileType=fileType, fileName=directory, leftBorder=leftBorder, rightBorder=rightBorder, bucketSize=bucketSize, 
+						exclusionZones=exclusionZones, exclusionZonesBorders=exclusionZonesBorders, graph=graphique, nomFichier=nomGraphe, 
+						savLog.txtC=logFile)
 data_bucket <- outputs[[1]]
 data_sample <- outputs[[2]]
 data_variable <- outputs[[3]]