comparison metams.r @ 3:c75532b75ba1 draft

Uploaded version 2.1.1

2:8e1b99a7d733

#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
# metams.r version="2.0"
#created by Yann GUITTON 
#use RI options

#Redirect all stdout to the log file
log_file=file("metams.log", open = "wt")
sink(log_file)
sink(log_file, type = "out")

source_local <- function(fname) {
    argv <- commandArgs(trailingOnly = FALSE)
    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
    source(paste(base_dir, fname, sep="/"))
}
print("step1")


listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
print("new version 2.0")


print(listArguments)


if (listArguments[["ri"]]!="NULL"){
    RIarg=read.table(listArguments[["ri"]])

       
print("Step QC plot")

#to do check if no peaks found
#Quality controls plots but only working in R (don't know why)
a<-plotUnknowns(resGC=resGC, unkn=unknarg) #use unknparam value

# create a mergpdf

#test
system(paste('gs  -o TICsBPCs_merged.pdf  -sDEVICE=pdfwrite  -dPDFSETTINGS=/prepress  *Cs_raw.pdf'))
system(paste('gs  -o GCMS_EIC.pdf  -sDEVICE=pdfwrite  -dPDFSETTINGS=/prepress  Unknown_*'))

rm(listArguments)

#saving R data in .Rdata file to save the variables used in the present tool
save.image(paste("runGC","RData",sep="."))

3:c75532b75ba1

#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
# metams.r version="2.1.1"
#created by Yann GUITTON 
#use RI options + add try on plotUnknown add session Info

#Redirect all stdout to the log file
log_file=file("metams.log", open = "wt")
sink(log_file)
sink(log_file, type = "out")

source_local <- function(fname) {
    argv <- commandArgs(trailingOnly = FALSE)
    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
    source(paste(base_dir, fname, sep="/"))
}
# print("step1")


listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
# print("new version 2.0")
## constants
##----------

modNamC <- "metaMS:runGC" ## module name


## log file
##---------
cat("\nStart of the '", modNamC, "' Galaxy module call: ",
format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")


cat("\n1) Parameters:\n")
print(listArguments)


if (listArguments[["ri"]]!="NULL"){
    RIarg=read.table(listArguments[["ri"]])

       
print("Step QC plot")

#to do check if no peaks found
#Quality controls plots but only working in R (don't know why)
a<-try(plotUnknowns(resGC=resGC, unkn=unknarg)); #use unknparam value
if(class(a) == "try-error") {
   pdf("Unknown_Error.pdf")
	plot.new()
	text(x=0.5,y=1,pos=1, labels="Error generating EICs\n please use none instead of a vector in plotUnknown")
   dev.off()
}
# create a mergpdf

#test
system(paste('gs  -o TICsBPCs_merged.pdf  -sDEVICE=pdfwrite  -dPDFSETTINGS=/prepress  *Cs_raw.pdf'))
system(paste('gs  -o GCMS_EIC.pdf  -sDEVICE=pdfwrite  -dPDFSETTINGS=/prepress  Unknown_*'))

rm(listArguments)

#saving R data in .Rdata file to save the variables used in the present tool
save.image(paste("runGC","RData",sep="."))

## Closing
##--------

cat("\nEnd of '", modNamC, "' Galaxy module call: ",
    as.character(Sys.time()), "\n", sep = "")

cat("\n\n\n============================================================================")
cat("\nAdditional information about the call:\n")
# cat("\n1) Parameters:\n")
# print(cbind(value = argVc))

cat("\n1) Session Info:\n")
sessioninfo <- sessionInfo()
cat(sessioninfo$R.version$version.string,"\n")
cat("Main packages:\n")
for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
cat("Other loaded packages:\n")
for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")

cat("============================================================================\n")

sink()

rm(list = ls())