annotate ReadFids_wrapper.R @ 6:6e837e9352a2 draft default tip

"planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 62fed9acaee7410de763b756cfa7de48ee258929"

#!/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())