Mercurial > repos > lecorguille > camera_annotate

comparison CAMERA_annotateDiffreport.r @ 25:4b9ab71be05e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58
author workflow4metabolomics
date Mon, 11 Sep 2023 22:40:34 +0000
parents abf1775ac14d
children
comparison
equal deleted inserted replaced
24:512c2b701d96 25:4b9ab71be05e
1 #!/usr/bin/env Rscript 1 #!/usr/bin/env Rscript
2 2
3 # ----- PACKAGE ----- 3 # ----- PACKAGE -----
4 cat("\tSESSION INFO\n") 4 cat("\tSESSION INFO\n")
5 5
6 #Import the different functions 6 # Import the different functions
7 source_local <- function(fname) { 7 source_local <- function(fname) {
8 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/")) 8 argv <- commandArgs(trailingOnly = FALSE)
9 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
10 source(paste(base_dir, fname, sep = "/"))
9 } 11 }
10 source_local("lib.r") 12 source_local("lib.r")
11 13
12 pkgs <- c("CAMERA", "multtest", "batch") 14 pkgs <- c("CAMERA", "multtest", "batch")
13 loadAndDisplayPackages(pkgs) 15 loadAndDisplayPackages(pkgs)
14 cat("\n\n"); 16 cat("\n\n")
15
16 # ----- ARGUMENTS ----- 17 # ----- ARGUMENTS -----
17 cat("\tARGUMENTS INFO\n") 18 cat("\tARGUMENTS INFO\n")
18 19
19 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects 20 args <- parseCommandArgs(evaluate = FALSE) # interpretation of arguments given in command line as an R list of objects
20 write.table(as.matrix(args), col.names = F, quote = F, sep = "\t") 21 write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
21 22
22 cat("\n\n"); 23 cat("\n\n")
23
24
25 # ----- PROCESSING INFILE ----- 24 # ----- PROCESSING INFILE -----
26 cat("\tINFILE PROCESSING INFO\n") 25 cat("\tINFILE PROCESSING INFO\n")
27 26
28 #image is an .RData file necessary to use xset variable given by previous tools 27 # image is an .RData file necessary to use xset variable given by previous tools
29 load(args$image); args$image <- NULL 28 load(args$image)
29 args$image <- NULL
30 30
31 cat("\n\n") 31 cat("\n\n")
32 32
33 33
34 # ----- ARGUMENTS PROCESSING ----- 34 # ----- ARGUMENTS PROCESSING -----
48 directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile) 48 directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile)
49 49
50 50
51 # Because so far CAMERA isn't compatible with the new XCMSnExp object 51 # Because so far CAMERA isn't compatible with the new XCMSnExp object
52 if (exists("xdata")) { 52 if (exists("xdata")) {
53 xset <- getxcmsSetObject(xdata) 53 xset <- getxcmsSetObject(xdata)
54 } 54 }
55 55
56 cat("\n\n") 56 cat("\n\n")
57 57
58 58
70 70
71 cat("\tXSET OBJECT INFO\n") 71 cat("\tXSET OBJECT INFO\n")
72 print(xa) 72 print(xa)
73 cat("\n\n") 73 cat("\n\n")
74 74
75 #saving R data in .Rdata file to save the variables used in the present tool 75 # saving R data in .Rdata file to save the variables used in the present tool
76 objects2save <- c("xa", "variableMetadata", "diffrep", "cAnnot", "listOFargs", "zipfile", "singlefile") 76 objects2save <- c("xa", "variableMetadata", "diffrep", "cAnnot", "listOFargs", "zipfile", "singlefile")
77 save(list = objects2save[objects2save %in% ls()], file = "annotatediff.RData") 77 save(list = objects2save[objects2save %in% ls()], file = "annotatediff.RData")
78 78
79 cat("\n\n") 79 cat("\n\n")
80 80