Mercurial > repos > lecorguille > xcms_xcmsset

comparison xcms_xcmsSet.r @ 35:3990a65b45a4 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
author workflow4metabolomics
date Mon, 03 Feb 2025 14:48:09 +0000
parents f5d51091cf84
children
comparison
equal deleted inserted replaced
34:6550698fe60f 35:3990a65b45a4
7 7
8 8
9 # ----- PACKAGE ----- 9 # ----- PACKAGE -----
10 cat("\tSESSION INFO\n") 10 cat("\tSESSION INFO\n")
11 11
12 #Import the different functions 12 # Import the different functions
13 source_local <- function(fname) { 13 source_local <- function(fname) {
14 argv <- commandArgs(trailingOnly = FALSE) 14 argv <- commandArgs(trailingOnly = FALSE)
15 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) 15 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
16 source(paste(base_dir, fname, sep = "/")) 16 source(paste(base_dir, fname, sep = "/"))
17 } 17 }
18 source_local("lib.r") 18 source_local("lib.r")
19 19
20 pkgs <- c("xcms", "batch") 20 pkgs <- c("xcms", "batch")
21 loadAndDisplayPackages(pkgs) 21 loadAndDisplayPackages(pkgs)
22 cat("\n\n") 22 cat("\n\n")
23 23
24 24
25 # ----- ARGUMENTS ----- 25 # ----- ARGUMENTS -----
26 cat("\tARGUMENTS INFO\n") 26 cat("\tARGUMENTS INFO\n")
27 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects 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") 28 write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
29 29
30 cat("\n\n") 30 cat("\n\n")
31 31
32 32
33 # ----- PROCESSING INFILE ----- 33 # ----- PROCESSING INFILE -----
34 cat("\tARGUMENTS PROCESSING INFO\n") 34 cat("\tARGUMENTS PROCESSING INFO\n")
35 35
36 #saving the commun parameters 36 # saving the commun parameters
37 BPPARAM <- MulticoreParam(1) 37 BPPARAM <- MulticoreParam(1)
38 if (!is.null(args$BPPARAM)) { 38 if (!is.null(args$BPPARAM)) {
39 BPPARAM <- MulticoreParam(args$BPPARAM) 39 BPPARAM <- MulticoreParam(args$BPPARAM)
40 } 40 }
41 register(BPPARAM) 41 register(BPPARAM)
42 42
43 #saving the specific parameters 43 # saving the specific parameters
44 if (!is.null(args$filterAcquisitionNum)) filterAcquisitionNumParam <- args$filterAcquisitionNum 44 if (!is.null(args$filterAcquisitionNum)) filterAcquisitionNumParam <- args$filterAcquisitionNum
45 if (!is.null(args$filterRt)) filterRtParam <- args$filterRt 45 if (!is.null(args$filterRt)) filterRtParam <- args$filterRt
46 if (!is.null(args$filterMz)) filterMzParam <- args$filterMz 46 if (!is.null(args$filterMz)) filterMzParam <- args$filterMz
47 if (!is.null(args$peaklist)) peaklistParam <- args$peaklist 47 if (!is.null(args$peaklist)) peaklistParam <- args$peaklist
48 48
49 method <- args$method 49 method <- args$method
50 50
51 if (!is.null(args$roiList)) { 51 if (!is.null(args$roiList)) {
52 cat("\t\troiList provided\n") 52 cat("\t\troiList provided\n")
53 args$roiList <- list(getDataFrameFromFile(args$roiList)) 53 args$roiList <- list(getDataFrameFromFile(args$roiList))
54 print(args$roiList) 54 print(args$roiList)
55 } 55 }
56 56
57 cat("\n\n") 57 cat("\n\n")
58 58
59 # ----- INFILE PROCESSING ----- 59 # ----- INFILE PROCESSING -----
60 cat("\tINFILE PROCESSING INFO\n") 60 cat("\tINFILE PROCESSING INFO\n")
61 61
62 #image is an .RData file necessary to use xset variable given by previous tools 62 # image is an .RData file necessary to use xset variable given by previous tools
63 load(args$image) 63 load(args$image)
64 if (!exists("raw_data")) stop("\n\nERROR: The RData doesn't contain any object called 'raw_data' which is provided by the tool: MSnbase readMSData") 64 if (!exists("raw_data")) stop("\n\nERROR: The RData doesn't contain any object called 'raw_data' which is provided by the tool: MSnbase readMSData")
65 65
66 # Handle infiles 66 # Handle infiles
67 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) 67 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
77 77
78 78
79 cat("\t\tCOMPUTE\n") 79 cat("\t\tCOMPUTE\n")
80 80
81 cat("\t\t\tApply filter[s] (if asked)\n") 81 cat("\t\t\tApply filter[s] (if asked)\n")
82 if (exists("filterAcquisitionNumParam")) raw_data <- filterAcquisitionNum(raw_data, filterAcquisitionNumParam[1]:filterAcquisitionNumParam[2]) 82 if (exists("filterAcquisitionNumParam")) raw_data <- filterAcquisitionNum(raw_data, filterAcquisitionNumParam[1]:filterAcquisitionNumParam[2])
83 if (exists("filterRtParam")) raw_data <- filterRt(raw_data, filterRtParam) 83 if (exists("filterRtParam")) raw_data <- filterRt(raw_data, filterRtParam)
84 if (exists("filterMzParam")) raw_data <- filterMz(raw_data, filterMzParam) 84 if (exists("filterMzParam")) raw_data <- filterMz(raw_data, filterMzParam)
85 #Apply this filter only if file contain MS and MSn 85 # Apply this filter only if file contain MS and MSn
86 if (length(unique(msLevel(raw_data))) != 1) { 86 if (length(unique(msLevel(raw_data))) != 1) {
87 raw_data <- filterMsLevel(raw_data, msLevel = 1) 87 raw_data <- filterMsLevel(raw_data, msLevel = 1)
88 } 88 }
89 89
90 cat("\t\t\tChromatographic peak detection\n") 90 cat("\t\t\tChromatographic peak detection\n")
91 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ... 91 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
92 args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))] 92 args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))]
101 # Create a sampleMetada file 101 # Create a sampleMetada file
102 sampleNamesList <- getSampleMetadata(xdata = xdata, sampleMetadataOutput = "sampleMetadata.tsv") 102 sampleNamesList <- getSampleMetadata(xdata = xdata, sampleMetadataOutput = "sampleMetadata.tsv")
103 103
104 # Create a chromPeaks table if required 104 # Create a chromPeaks table if required
105 if (exists("peaklistParam")) { 105 if (exists("peaklistParam")) {
106 if (peaklistParam) { 106 if (peaklistParam) {
107 cat("\nCreating the chromatographic peaks' table...\n") 107 cat("\nCreating the chromatographic peaks' table...\n")
108 write.table(chromPeaks(xdata), file = "chromPeak_table.tsv", sep = "\t", quote = FALSE, row.names = FALSE) 108 write.table(chromPeaks(xdata), file = "chromPeak_table.tsv", sep = "\t", quote = FALSE, row.names = FALSE)
109 } 109 }
110 } 110 }
111 111
112 cat("\n\n") 112 cat("\n\n")
113 113
114 # ----- EXPORT ----- 114 # ----- EXPORT -----
121 # Get the legacy xcmsSet object 121 # Get the legacy xcmsSet object
122 xset <- getxcmsSetObject(xdata) 122 xset <- getxcmsSetObject(xdata)
123 print(xset) 123 print(xset)
124 cat("\n\n") 124 cat("\n\n")
125 125
126 #saving R data in .Rdata file to save the variables used in the present tool 126 # saving R data in .Rdata file to save the variables used in the present tool
127 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") 127 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
128 save(list = objects2save[objects2save %in% ls()], file = "xcmsSet.RData") 128 save(list = objects2save[objects2save %in% ls()], file = "xcmsSet.RData")
129 129
130 130
131 cat("\tDONE\n") 131 cat("\tDONE\n")