Mercurial > repos > lecorguille > msnbase_readmsdata
comparison msnbase_readmsdata.r @ 0:728ebc7ae7dd draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author | lecorguille |
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date | Tue, 18 Sep 2018 16:04:51 -0400 |
parents | |
children | 2a69f9923a70 |
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-1:000000000000 | 0:728ebc7ae7dd |
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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){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } | |
14 source_local("lib.r") | |
15 source_local("lib-xcms3.x.x.r") | |
16 | |
17 pkgs <- c("MSnbase","batch") | |
18 loadAndDisplayPackages(pkgs) | |
19 cat("\n\n"); | |
20 | |
21 | |
22 # ----- ARGUMENTS ----- | |
23 cat("\tARGUMENTS INFO\n") | |
24 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects | |
25 write.table(as.matrix(args), col.names=F, quote=F, sep='\t') | |
26 | |
27 cat("\n\n") | |
28 | |
29 | |
30 # ----- PROCESSING INFILE ----- | |
31 cat("\tARGUMENTS PROCESSING INFO\n") | |
32 | |
33 | |
34 cat("\n\n") | |
35 | |
36 # ----- INFILE PROCESSING ----- | |
37 cat("\tINFILE PROCESSING INFO\n") | |
38 | |
39 # Handle infiles | |
40 if (!exists("singlefile")) singlefile <- NULL | |
41 if (!exists("zipfile")) zipfile <- NULL | |
42 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) | |
43 zipfile <- rawFilePath$zipfile | |
44 singlefile <- rawFilePath$singlefile | |
45 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) | |
46 | |
47 # Check some character issues | |
48 md5sumList <- list("origin" = getMd5sum(directory)) | |
49 checkXmlStructure(directory) | |
50 checkFilesCompatibilityWithXcms(directory) | |
51 | |
52 | |
53 cat("\n\n") | |
54 | |
55 | |
56 # ----- MAIN PROCESSING INFO ----- | |
57 cat("\tMAIN PROCESSING INFO\n") | |
58 | |
59 | |
60 cat("\t\tCOMPUTE\n") | |
61 | |
62 ## Get the full path to the files | |
63 files <- getMSFiles(directory) | |
64 | |
65 cat("\t\t\tCreate a phenodata data.frame\n") | |
66 s_groups <- sapply(files, function(x) tail(unlist(strsplit(dirname(x),"/")), n=1)) | |
67 s_name <- tools::file_path_sans_ext(basename(files)) | |
68 pd <- data.frame(sample_name=s_name, sample_group=s_groups, stringsAsFactors=FALSE) | |
69 print(pd) | |
70 | |
71 cat("\t\t\tLoad Raw Data\n") | |
72 raw_data <- readMSData(files=files, pdata = new("NAnnotatedDataFrame", pd), mode="onDisk") | |
73 | |
74 # Transform the files absolute pathways into relative pathways | |
75 raw_data@processingData@files <- sub(paste(getwd(), "/", sep="") , "", raw_data@processingData@files) | |
76 | |
77 # Create a sampleMetada file | |
78 sampleNamesList <- getSampleMetadata(xdata=raw_data, sampleMetadataOutput="sampleMetadata.tsv") | |
79 | |
80 cat("\t\t\tCompute and Store TIC and BPI\n") | |
81 chromTIC <- chromatogram(raw_data, aggregationFun = "sum") | |
82 chromBPI <- chromatogram(raw_data, aggregationFun = "max") | |
83 | |
84 cat("\n\n") | |
85 | |
86 # ----- EXPORT ----- | |
87 | |
88 cat("\tMSnExp OBJECT INFO\n") | |
89 print(raw_data) | |
90 cat("\t\tphenoData\n") | |
91 print(raw_data@phenoData@data) | |
92 cat("\n\n") | |
93 | |
94 #saving R data in .Rdata file to save the variables used in the present tool | |
95 objects2save <- c("raw_data", "zipfile", "singlefile", "md5sumList", "sampleNamesList", "chromTIC", "chromBPI") | |
96 save(list=objects2save[objects2save %in% ls()], file="readmsdata.RData") | |
97 | |
98 | |
99 cat("\tDONE\n") |