diff NmrNormalization_wrapper.R @ 3:966fcf7ae66e draft

planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NmrNormalization_wrapper.R	Thu Oct 26 06:01:14 2017 -0400
@@ -0,0 +1,139 @@
+#!/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
+## [e-mail]
+
+runExampleL <- FALSE
+
+
+##------------------------------
+## Options
+##------------------------------
+strAsFacL <- options()$stringsAsFactors
+options(stringsAsFactors = FALSE)
+
+
+##------------------------------
+## Libraries laoding
+##------------------------------
+# For parseCommandArgs function
+library(batch) 
+
+# 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")
+rownames(data) <- data[,1]
+data <- data[,-1]
+
+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 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("Bucket",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 = "")
+
+options(stringsAsFactors = strAsFacL)
+
+rm(list = ls())