Mercurial > repos > lecorguille > ipo

comparison ipo4xcmsSet.r @ 2:8e5f667359cb draft default tip

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planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
author workflow4metabolomics
date Mon, 11 Sep 2023 22:37:32 +0000
parents ae8de756dfcf
children
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1:ae8de756dfcf 2:8e5f667359cb
1 #!/usr/bin/env Rscript 1 #!/usr/bin/env Rscript
2 #Authors Gildas Le Corguille and Yann Guitton 2 # Authors Gildas Le Corguille and Yann Guitton
3 3
4 4
5 # ----- PACKAGE ----- 5 # ----- PACKAGE -----
6 cat("\tSESSION INFO\n") 6 cat("\tSESSION INFO\n")
7 7
8 #Import the different functions 8 # Import the different functions
9 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } 9 source_local <- function(fname) {
10 argv <- commandArgs(trailingOnly = FALSE)
11 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
12 source(paste(base_dir, fname, sep = "/"))
13 }
10 source_local("lib.r") 14 source_local("lib.r")
11 15
12 pkgs <- c("IPO","batch") 16 pkgs <- c("IPO", "batch")
13 loadAndDisplayPackages(pkgs) 17 loadAndDisplayPackages(pkgs)
14 cat("\n\n"); 18 cat("\n\n")
15
16
17 # ----- ARGUMENTS ----- 19 # ----- ARGUMENTS -----
18 cat("\tARGUMENTS INFO\n") 20 cat("\tARGUMENTS INFO\n")
19 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects 21 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') 22 write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
21 23
22 cat("\n\n"); 24 cat("\n\n")
23
24 # ----- PROCESSING INFILE ----- 25 # ----- PROCESSING INFILE -----
25 cat("\tARGUMENTS PROCESSING INFO\n") 26 cat("\tARGUMENTS PROCESSING INFO\n")
26 options(bitmapType='cairo') 27 options(bitmapType = "cairo")
27 28
28 samplebyclass = 2 29 samplebyclass <- 2
29 if (!is.null(args$samplebyclass)){ 30 if (!is.null(args$samplebyclass)) {
30 samplebyclass = args$samplebyclass; args$samplebyclass=NULL 31 samplebyclass <- args$samplebyclass
32 args$samplebyclass <- NULL
31 } 33 }
32 34
33 # ----- INFILE PROCESSING ----- 35 # ----- INFILE PROCESSING -----
34 cat("\tINFILE PROCESSING INFO\n") 36 cat("\tINFILE PROCESSING INFO\n")
35 37
36 # Handle infiles 38 # Handle infiles
37 if (!exists("singlefile")) singlefile <- NULL 39 if (!exists("singlefile")) singlefile <- NULL
38 rawFilePath <- getRawfilePathFromArguments(singlefile, NULL, args) 40 rawFilePath <- getRawfilePathFromArguments(singlefile, NULL, args)
39 singlefile <- rawFilePath$singlefile 41 singlefile <- rawFilePath$singlefile
40 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, NULL) 42 directory <- retrieveRawfileInWD(singlefile, NULL)
41 43
42 # Check some character issues 44 # Check some character issues
43 checkXmlStructure(directory) 45 checkXmlStructure(directory)
44 46
45 cat("\n\n") 47 cat("\n\n")
49 51
50 # ----- MAIN PROCESSING INFO ----- 52 # ----- MAIN PROCESSING INFO -----
51 cat("\tMAIN PROCESSING INFO\n") 53 cat("\tMAIN PROCESSING INFO\n")
52 54
53 55
54 xset = ipo4xcmsSet(directory, "IPO_parameters4xcmsSet.tsv", args, samplebyclass) 56 xset <- ipo4xcmsSet(directory, "IPO_parameters4xcmsSet.tsv", args, samplebyclass)
55 57
56 58
57 59
58 cat("\n\n") 60 cat("\n\n")
59 61
60 62
61 # ----- EXPORT ----- 63 # ----- EXPORT -----
62 64
63 cat("\tXSET OBJECT INFO\n") 65 cat("\tXSET OBJECT INFO\n")
64 print(xset) 66 print(xset)
65 #delete the parameters to avoid the passage to the next tool in .RData image 67 # delete the parameters to avoid the passage to the next tool in .RData image
66 68
67 69
68 #saving R data in .Rdata file to save the variables used in the present tool 70 # saving R data in .Rdata file to save the variables used in the present tool
69 objects2save = c("xset", "singlefile") 71 objects2save <- c("xset", "singlefile")
70 save(list=objects2save[objects2save %in% ls()], file="ipo4xcmsSet.RData") 72 save(list = objects2save[objects2save %in% ls()], file = "ipo4xcmsSet.RData")
71 73
72 cat("\n\n") 74 cat("\n\n")
73 75
74 76
75 cat("\tDONE\n") 77 cat("\tDONE\n")
76