diff nmr_preprocessing/ReadFids_wrapper.R @ 2:7304ec2c9ab7 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nmr_preprocessing/ReadFids_wrapper.R	Mon Jul 30 10:33:03 2018 -0400
@@ -0,0 +1,158 @@
+#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
+
+## 08122016_ReadFids_wrapper.R
+## Manon Martin
+## [e-mail]
+
+##======================================================
+##======================================================
+# Preamble
+##======================================================
+##======================================================
+
+runExampleL <- FALSE
+
+
+##------------------------------
+## Options
+##------------------------------
+strAsFacL <- options()$stringsAsFactors
+options(stringsAsFactors = FALSE)
+options(warn=1)
+
+##------------------------------
+## Libraries laoding
+##------------------------------
+library(batch) 
+library(ggplot2)
+library(gridExtra)
+library(reshape2)
+
+
+# R script call
+source_local <- function(fname)
+{
+  argv <- commandArgs(trailingOnly = FALSE)
+  base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+  source(paste(base_dir, fname, sep="/"))
+}
+#Import the different functions
+source_local("ReadFids_script.R")
+source_local("DrawFunctions.R")
+##------------------------------
+## Errors ?????????????????????
+##------------------------------
+
+
+##------------------------------
+## Constants
+##------------------------------
+topEnvC <- environment()
+flagC <- "\n"
+
+
+##------------------------------
+## Script
+##------------------------------
+if(!runExampleL)
+  argLs <- parseCommandArgs(evaluate=FALSE)
+
+sink(argLs$logOut)
+
+##======================================================
+##======================================================
+## Parameters Loading
+##======================================================
+##======================================================
+
+	## Inputs
+		# Path
+			## Bruker FIDs
+fileType="Bruker"
+zipfile= argLs[["fidzipfile"]]
+directory=unzip(zipfile, list=F)
+path=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/")
+
+
+# other inputs from ReadFids
+l = argLs[["title_line"]]
+subdirs <- argLs[["subdirectories"]]
+dirs.names <- argLs[["dirs_names"]]
+
+
+# Outputs
+# dataMatrix <- argLs[["dataMatrix"]]
+# sampleMetadata <- argLs[["sampleMetadata"]]
+logOut <- argLs[["logOut"]]
+nomGraphe <- argLs[["graphOut"]]
+	
+
+
+## Checking arguments
+##-------------------
+error.stock <- "\n"
+
+if(length(error.stock) > 1)
+  stop(error.stock)
+
+
+
+##======================================================
+##======================================================
+## Computation
+##======================================================
+##======================================================
+sink(logOut,append=TRUE)
+
+if(length(warnings())>0){ # or !is.null(warnings())
+  print("something happened")
+}
+
+## Starting
+cat("\nStart of 'ReadFids' Galaxy module call: ", as.character(Sys.time()), "\n\n", sep = "")
+
+outputs <- ReadFids(path = path, l=l, subdirs = subdirs, dirs.names = dirs.names) 
+
+data_matrix <- outputs[["Fid_data"]] # Data matrix
+data_sample <- outputs[["Fid_info"]] # Sample metadata
+
+
+
+pdf(nomGraphe, onefile = TRUE, width = 13, height = 13)
+title = "Raw FID data"
+DrawSignal(data_matrix, subtype = "stacked",
+             ReImModArg = c(TRUE, FALSE, FALSE, FALSE), vertical = T,
+             xlab = "Frequency", num.stacked = 4,
+             main = title, createWindow=FALSE)
+invisible(dev.off())
+
+##======================================================
+##======================================================
+## Saving
+##======================================================
+##======================================================
+
+# Data matrix
+write.table(data_matrix,file=argLs$dataMatrix, quote=FALSE, row.names=TRUE, sep="\t", col.names=TRUE)
+
+# Sample metadata
+write.table(data_sample,file=argLs$sampleMetadata, quote=FALSE, row.names=TRUE, sep="\t", col.names=TRUE)
+
+# log file
+# write.table(t(data.frame(argLs)), file = argLs$logOut, col.names = FALSE, quote=FALSE)
+
+# input arguments
+cat("\n INPUT and OUTPUT ARGUMENTS :\n")
+
+argLs
+
+## Ending
+
+cat("\nEnd of 'ReadFids' Galaxy module call: ", as.character(Sys.time()), sep = "")
+
+sink()
+
+
+options(stringsAsFactors = strAsFacL)
+
+rm(list = ls())
\ No newline at end of file