Mercurial > repos > lecorguille > xcms_retcor
comparison xcms_retcor.r @ 27:8242376d9f35 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
author | workflow4metabolomics |
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date | Thu, 14 Mar 2024 15:35:44 +0000 |
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26:36480435e92b | 27:8242376d9f35 |
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1 #!/usr/bin/env Rscript | |
2 | |
3 # ----- LOG FILE ----- | |
4 log_file <- file("log.txt", open = "wt") | |
5 sink(log_file) | |
6 sink(log_file, type = "output") | |
7 | |
8 | |
9 # ----- PACKAGE ----- | |
10 cat("\tSESSION INFO\n") | |
11 | |
12 #Import the different functions | |
13 source_local <- function(fname) { | |
14 argv <- commandArgs(trailingOnly = FALSE) | |
15 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | |
16 source(paste(base_dir, fname, sep = "/")) | |
17 } | |
18 source_local("lib.r") | |
19 | |
20 pkgs <- c("xcms", "batch", "RColorBrewer") | |
21 loadAndDisplayPackages(pkgs) | |
22 cat("\n\n") | |
23 | |
24 | |
25 # ----- ARGUMENTS ----- | |
26 cat("\tARGUMENTS INFO\n") | |
27 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects | |
28 write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t") | |
29 | |
30 cat("\n\n") | |
31 | |
32 # ----- PROCESSING INFILE ----- | |
33 cat("\tARGUMENTS PROCESSING INFO\n") | |
34 | |
35 #saving the specific parameters | |
36 method <- args$method | |
37 | |
38 cat("\n\n") | |
39 | |
40 | |
41 # ----- ARGUMENTS PROCESSING ----- | |
42 cat("\tINFILE PROCESSING INFO\n") | |
43 | |
44 #image is an .RData file necessary to use xset variable given by previous tools | |
45 load(args$image) | |
46 args$image <- NULL | |
47 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") | |
48 | |
49 # Handle infiles | |
50 if (!exists("singlefile")) singlefile <- NULL | |
51 if (!exists("zipfile")) zipfile <- NULL | |
52 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) | |
53 zipfile <- rawFilePath$zipfile | |
54 singlefile <- rawFilePath$singlefile | |
55 | |
56 cat("\n\n") | |
57 | |
58 | |
59 # ----- MAIN PROCESSING INFO ----- | |
60 cat("\tMAIN PROCESSING INFO\n") | |
61 | |
62 | |
63 cat("\t\tCOMPUTE\n") | |
64 | |
65 cat("\t\t\tAlignment/Retention Time correction\n") | |
66 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ... | |
67 args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))] | |
68 | |
69 adjustRtimeParam <- do.call(paste0(method, "Param"), args) | |
70 print(adjustRtimeParam) | |
71 | |
72 if (hasAdjustedRtime(xdata)) { | |
73 cat("WARNING: a retention time ajustment had already been applied to your data.\nThe function applyAdjustedRtime was processed to cumulate the ajustment") | |
74 cat("Replace raw retention times with adjusted retention times.\n") | |
75 xdata <- applyAdjustedRtime(xdata) | |
76 } | |
77 xdata <- adjustRtime(xdata, param = adjustRtimeParam) | |
78 | |
79 cat("\n\n") | |
80 | |
81 | |
82 # -- TIC -- | |
83 cat("\t\tDRAW GRAPHICS\n") | |
84 getPlotAdjustedRtime(xdata) | |
85 | |
86 cat("\n\n") | |
87 | |
88 # ----- EXPORT ----- | |
89 | |
90 cat("\tXCMSnExp OBJECT INFO\n") | |
91 print(xdata) | |
92 cat("\n\n") | |
93 | |
94 cat("\txcmsSet OBJECT INFO\n") | |
95 # Get the legacy xcmsSet object | |
96 xset <- getxcmsSetObject(xdata) | |
97 print(xset) | |
98 cat("\n\n") | |
99 | |
100 #saving R data in .Rdata file to save the variables used in the present tool | |
101 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") | |
102 save(list = objects2save[objects2save %in% ls()], file = "retcor.RData") | |
103 | |
104 cat("\n\n") | |
105 | |
106 | |
107 cat("\tDONE\n") |