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Try to correct the indentation problem with lintr
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@DamienCode404
DamienCode404 committed Oct 23, 2024
1 parent d3b6bd2 commit 217570f
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188 changes: 94 additions & 94 deletions tools/metams/metaMS_plot/metaMS_plot.r
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Original file line number Diff line number Diff line change
@@ -1,39 +1,39 @@
#!/usr/bin/env Rscript
# metaMS_plot.r version="1.0.0"
#created by Yann GUITTON and updated by Julien SAINT-VANNE
# created by Yann GUITTON and updated by Julien SAINT-VANNE


# ----- LOG FILE -----
#log_file <- file("log.txt", open = "wt")
#sink(log_file)
#sink(log_file, type = "output")
# log_file <- file("log.txt", open = "wt")
# sink(log_file)
# sink(log_file, type = "output")


# ----- PACKAGE -----
cat("\tSESSION INFO\n")

#Import the different functions
# Import the different functions
source_local <- function(fname) {
argv <- commandArgs(trailingOnly = FALSE)
base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
source(paste(base_dir, fname, sep="/"))
argv <- commandArgs(trailingOnly = FALSE)
base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
source(paste(base_dir, fname, sep = "/"))
}
source_local("lib_metams.r")

pkgs <- c("metaMS","batch") #"batch" necessary for parseCommandArgs function
pkgs <- c("metaMS", "batch") # "batch" necessary for parseCommandArgs function
loadAndDisplayPackages(pkgs)

cat("\n")

modNamC <- "plot_metaMS" ## module name

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


# ----- ARGUMENTS -----
cat("\tARGUMENTS INFO\n\n")
args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
#write.table(as.matrix(args), col.names=F, quote=F, sep='\t\t')
args <- parseCommandArgs(evaluate = FALSE) # interpretation of arguments given in command line as an R list of objects
# write.table(as.matrix(args), col.names=F, quote=F, sep='\t\t')
print(cbind(value = unlist(args)))


Expand All @@ -44,31 +44,31 @@ cat("\n\n\tARGUMENTS PROCESSING INFO\n\n")
load(args$metaMS)
if (!exists("resGC")) stop("\n\nERROR: The RData doesn't contain any object called 'resGC' which is provided by the tool: new_metaMS.runGC")

if(args$selecteic) {
#Unknown EIC parameter
if (args$unkn[1] != "NULL") {
#When unkn = 0 user want to process all unknowns
if(args$unkn[1] == 0) {
args$unkn <- c(1:nrow(resGC$PeakTable))
print("User want to process on all unknown(s) found in metaMS process")
}
#TODO find the biggest number of unkn ask by user cause it can write "1,15,9,8" with a max of 11 unkn. With this code it finds the 8 and it will pass
#Verify that there is not more user's unkn than metaMS unkn (find in resGC$PeakTable)
cat("Number of unknown after metaMS process :",nrow(resGC$PeakTable),"\n")
cat("Number of the last unknown ask by user :",args$unkn[length(args$unkn)],"\n")
cat("Number of unknown ask by user :",length(args$unkn),"\n")
if(args$unkn[length(args$unkn)] <= nrow(resGC$PeakTable)) {
unknarg <- args$unkn
} else {
error_message="Too much unkn compare metaMS results"
print(error_message)
stop(error_message)
}
if (args$selecteic) {
# Unknown EIC parameter
if (args$unkn[1] != "NULL") {
# When unkn = 0 user want to process all unknowns
if (args$unkn[1] == 0) {
args$unkn <- c(1:nrow(resGC$PeakTable))
print("User want to process on all unknown(s) found in metaMS process")
}
# TODO find the biggest number of unkn ask by user cause it can write "1,15,9,8" with a max of 11 unkn. With this code it finds the 8 and it will pass
# Verify that there is not more user's unkn than metaMS unkn (find in resGC$PeakTable)
cat("Number of unknown after metaMS process :", nrow(resGC$PeakTable), "\n")
cat("Number of the last unknown ask by user :", args$unkn[length(args$unkn)], "\n")
cat("Number of unknown ask by user :", length(args$unkn), "\n")
if (args$unkn[length(args$unkn)] <= nrow(resGC$PeakTable)) {
unknarg <- args$unkn
} else {
error_message <- "No EIC selected !"
print(error_message)
stop(error_message)
error_message <- "Too much unkn compare metaMS results"
print(error_message)
stop(error_message)
}
} else {
error_message <- "No EIC selected !"
print(error_message)
stop(error_message)
}
}

cat("\n\n")
Expand All @@ -92,67 +92,67 @@ cat("\n\n\tMAIN PROCESSING INFO\n")

cat("\t\tCOMPUTE\n")

#Use getTIC2s and getBPC2s because getTICs and getBPCs can exists due to transfert of function in Rdata

if(!is.null(singlefile)) {
files <- paste("./",names(singlefile),sep="")
#WARNING if user has CDF files (not yet good for plotting)
if(MSnbase:::isCdfFile(files)){
warning_message <- "You have CDF files, for the moment you can't obtain plot after runGC! A new update will follow with the good correction\n"
warning(warning_message)
cat(paste("\n","/!\\Warning/!\\",warning_message,sep="\n"))
# Use getTIC2s and getBPC2s because getTICs and getBPCs can exists due to transfert of function in Rdata

if (!is.null(singlefile)) {
files <- paste("./", names(singlefile), sep = "")
# WARNING if user has CDF files (not yet good for plotting)
if (MSnbase:::isCdfFile(files)) {
warning_message <- "You have CDF files, for the moment you can't obtain plot after runGC! A new update will follow with the good correction\n"
warning(warning_message)
cat(paste("\n", "/!\\Warning/!\\", warning_message, sep = "\n"))
}
if (!is.null(files)) {
if (args$selectbpc) {
cat("\n\tProcessing BPC(s) from XCMS files...\n")
c <- getBPC2s(files = files, xset = xset, rt = "raw", pdfname = "BPCs_raw.pdf")
cat("BPC(s) created...\n")
}
if(!is.null(files)){
if(args$selectbpc){
cat("\n\tProcessing BPC(s) from XCMS files...\n")
c <- getBPC2s(files = files, xset = xset, rt="raw", pdfname="BPCs_raw.pdf")
cat("BPC(s) created...\n")
}
if(args$selecttic){
cat("\n\tProcessing TIC(s) from XCMS files...\n")
b <- getTIC2s(files = files, xset = xset, rt="raw", pdfname="TICs_raw.pdf")
cat("TIC(s) created...\n")
}
if(args$selecteic){
cat("\n\tProcessing EIC(s) from XCMS files...\n")
cat(length(unknarg),"unknown(s) will be process !\n")
plotUnknowns(resGC=resGC, unkn=unknarg, DB=DBgc, fileFrom="singlefile")
cat("EIC(s) created...\n")
#Merge pdf
system(paste('gs -o GCMS_EIC.pdf -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress Unknown_*.pdf'))
}
} else {
error_message <- paste("Can't find",files,"!")
print(error_message)
stop(error_message)
if (args$selecttic) {
cat("\n\tProcessing TIC(s) from XCMS files...\n")
b <- getTIC2s(files = files, xset = xset, rt = "raw", pdfname = "TICs_raw.pdf")
cat("TIC(s) created...\n")
}
if (args$selecteic) {
cat("\n\tProcessing EIC(s) from XCMS files...\n")
cat(length(unknarg), "unknown(s) will be process !\n")
plotUnknowns(resGC = resGC, unkn = unknarg, DB = DBgc, fileFrom = "singlefile")
cat("EIC(s) created...\n")
# Merge pdf
system(paste("gs -o GCMS_EIC.pdf -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress Unknown_*.pdf"))
}
} else {
error_message <- paste("Can't find", files, "!")
print(error_message)
stop(error_message)
}
}
if(!is.null(zipfile)) {
files <- getMSFiles(directory)
if(!is.null(files)) {
if(args$selectbpc) {
cat("\n\tProcessing BPC(s) from raw files...\n")
c <- getBPC2s(files = files, rt="raw", pdfname="BPCs_raw.pdf")
cat("BPC(s) created...\n")
}
if(args$selecttic) {
cat("\n\tProcessing TIC(s) from raw files...\n")
b <- getTIC2s(files = files, rt="raw", pdfname="TICs_raw.pdf")
cat("TIC(s) created...\n")
}
if(args$selecteic) {
cat("\n\tProcessing EIC(s) from XCMS files...\n")
cat(length(unknarg),"unknown(s) will be process !\n")
plotUnknowns(resGC=resGC, unkn=unknarg, DB=DBgc, fileFrom="zipfile")
cat("EIC(s) created...\n")
#Merge pdf
system(paste('gs -sOutputFile=GCMS_EIC.pdf -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress Unknown_*.pdf'))
}
} else {
error_message <- paste("Can't find",files,"!")
print(error_message)
stop(error_message)
}
if (!is.null(zipfile)) {
files <- getMSFiles(directory)
if (!is.null(files)) {
if (args$selectbpc) {
cat("\n\tProcessing BPC(s) from raw files...\n")
c <- getBPC2s(files = files, rt = "raw", pdfname = "BPCs_raw.pdf")
cat("BPC(s) created...\n")
}
if (args$selecttic) {
cat("\n\tProcessing TIC(s) from raw files...\n")
b <- getTIC2s(files = files, rt = "raw", pdfname = "TICs_raw.pdf")
cat("TIC(s) created...\n")
}
if (args$selecteic) {
cat("\n\tProcessing EIC(s) from XCMS files...\n")
cat(length(unknarg), "unknown(s) will be process !\n")
plotUnknowns(resGC = resGC, unkn = unknarg, DB = DBgc, fileFrom = "zipfile")
cat("EIC(s) created...\n")
# Merge pdf
system(paste("gs -sOutputFile=GCMS_EIC.pdf -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress Unknown_*.pdf"))
}
} else {
error_message <- paste("Can't find", files, "!")
print(error_message)
stop(error_message)
}
}

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