diff CAMERA_annotateDiffreport.r @ 23:abf1775ac14d draft

"planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998"

--- a/CAMERA_annotateDiffreport.r	Mon Mar 30 09:27:57 2020 -0400
+++ b/CAMERA_annotateDiffreport.r	Thu Apr 22 10:27:38 2021 +0000
@@ -4,18 +4,20 @@
 cat("\tSESSION INFO\n")
 
 #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="/")) }
+source_local <- function(fname) {
+  argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/"))
+}
 source_local("lib.r")
 
-pkgs=c("CAMERA","multtest","batch")
+pkgs <- c("CAMERA", "multtest", "batch")
 loadAndDisplayPackages(pkgs)
 cat("\n\n");
 
 # ----- ARGUMENTS -----
 cat("\tARGUMENTS INFO\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')
+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")
 
 cat("\n\n");
 
@@ -24,7 +26,7 @@
 cat("\tINFILE PROCESSING INFO\n")
 
 #image is an .RData file necessary to use xset variable given by previous tools
-load(args$image); args$image=NULL
+load(args$image); args$image <- NULL
 
 cat("\n\n")
 
@@ -33,21 +35,21 @@
 cat("\tARGUMENTS PROCESSING INFO\n")
 
 # Save arguments to generate a report
-if (!exists("listOFargs")) listOFargs=list()
-listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_annotatediff")]] = args
+if (!exists("listOFargs")) listOFargs <- list()
+listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_annotatediff")]] <- args
 
 # We unzip automatically the chromatograms from the zip files.
-if (!exists("zipfile")) zipfile=NULL
-if (!exists("singlefile")) singlefile=NULL
-rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, args)
-zipfile = rawFilePath$zipfile
-singlefile = rawFilePath$singlefile
-args = rawFilePath$args
-directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
+if (!exists("zipfile")) zipfile <- NULL
+if (!exists("singlefile")) singlefile <- NULL
+rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
+zipfile <- rawFilePath$zipfile
+singlefile <- rawFilePath$singlefile
+args <- rawFilePath$args
+directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
 
 
 # Because so far CAMERA isn't compatible with the new XCMSnExp object
-if (exists("xdata")){
+if (exists("xdata")) {
     xset <- getxcmsSetObject(xdata)
 }
 
@@ -57,10 +59,10 @@
 # ----- PROCESSING INFO -----
 cat("\tMAIN PROCESSING INFO\n")
 
-results_list=annotatediff(xset=xset,args=args,variableMetadataOutput="variableMetadata.tsv")
-xa=results_list$xa
-diffrep=results_list$diffrep
-variableMetadata=results_list$variableMetadata
+results_list <- annotatediff(xset = xset, args = args, variableMetadataOutput = "variableMetadata.tsv")
+xa <- results_list$xa
+diffrep <- results_list$diffrep
+variableMetadata <- results_list$variableMetadata
 
 cat("\n\n")
 
@@ -71,8 +73,8 @@
 cat("\n\n")
 
 #saving R data in .Rdata file to save the variables used in the present tool
-objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFargs","zipfile","singlefile")
-save(list=objects2save[objects2save %in% ls()], file="annotatediff.RData")
+objects2save <- c("xa", "variableMetadata", "diffrep", "cAnnot", "listOFargs", "zipfile", "singlefile")
+save(list = objects2save[objects2save %in% ls()], file = "annotatediff.RData")
 
 cat("\n\n")