Mercurial > repos > lecorguille > xcms_xcmsset

comparison xcms_xcmsSet.r @ 32:b02d1992a43a draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author workflow4metabolomics
date Wed, 07 Apr 2021 16:47:14 +0000
parents eb15a3841da4
children f5d51091cf84
comparison
equal deleted inserted replaced
31:eb15a3841da4 32:b02d1992a43a
1 #!/usr/bin/env Rscript 1 #!/usr/bin/env Rscript
2 2
3 # ----- LOG FILE ----- 3 # ----- LOG FILE -----
4 log_file <- file("log.txt", open="wt") 4 log_file <- file("log.txt", open = "wt")
5 sink(log_file) 5 sink(log_file)
6 sink(log_file, type = "output") 6 sink(log_file, type = "output")
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){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } 13 source_local <- function(fname) {
14 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/"))
15 }
14 source_local("lib.r") 16 source_local("lib.r")
15 17
16 pkgs <- c("xcms","batch") 18 pkgs <- c("xcms", "batch")
17 loadAndDisplayPackages(pkgs) 19 loadAndDisplayPackages(pkgs)
18 cat("\n\n"); 20 cat("\n\n");
19 21
20 22
21 # ----- ARGUMENTS ----- 23 # ----- ARGUMENTS -----
22 cat("\tARGUMENTS INFO\n") 24 cat("\tARGUMENTS INFO\n")
23 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects 25 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
24 write.table(as.matrix(args), col.names=F, quote=F, sep='\t') 26 write.table(as.matrix(args), col.names = F, quote = F, sep = "\t")
25 27
26 cat("\n\n") 28 cat("\n\n")
27 29
28 30
29 # ----- PROCESSING INFILE ----- 31 # ----- PROCESSING INFILE -----
30 cat("\tARGUMENTS PROCESSING INFO\n") 32 cat("\tARGUMENTS PROCESSING INFO\n")
31 33
32 #saving the commun parameters 34 #saving the commun parameters
33 BPPARAM <- MulticoreParam(1) 35 BPPARAM <- MulticoreParam(1)
34 if (!is.null(args$BPPARAM)){ 36 if (!is.null(args$BPPARAM)) {
35 BPPARAM <- MulticoreParam(args$BPPARAM) 37 BPPARAM <- MulticoreParam(args$BPPARAM)
36 } 38 }
37 register(BPPARAM) 39 register(BPPARAM)
38 40
39 #saving the specific parameters 41 #saving the specific parameters
42 if (!is.null(args$filterMz)) filterMzParam <- args$filterMz 44 if (!is.null(args$filterMz)) filterMzParam <- args$filterMz
43 if (!is.null(args$peaklist)) peaklistParam <- args$peaklist 45 if (!is.null(args$peaklist)) peaklistParam <- args$peaklist
44 46
45 method <- args$method 47 method <- args$method
46 48
47 if (!is.null(args$roiList)){ 49 if (!is.null(args$roiList)) {
48 cat("\t\troiList provided\n") 50 cat("\t\troiList provided\n")
49 args$roiList <- list(getDataFrameFromFile(args$roiList)) 51 args$roiList <- list(getDataFrameFromFile(args$roiList))
50 print(args$roiList) 52 print(args$roiList)
51 } 53 }
52 54
58 #image is an .RData file necessary to use xset variable given by previous tools 60 #image is an .RData file necessary to use xset variable given by previous tools
59 load(args$image) 61 load(args$image)
60 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") 62 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")
61 63
62 # Handle infiles 64 # Handle infiles
63 rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args) 65 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
64 zipfile <- rawFilePath$zipfile 66 zipfile <- rawFilePath$zipfile
65 singlefile <- rawFilePath$singlefile 67 singlefile <- rawFilePath$singlefile
66 68
67 69
68 cat("\n\n") 70 cat("\n\n")
77 cat("\t\t\tApply filter[s] (if asked)\n") 79 cat("\t\t\tApply filter[s] (if asked)\n")
78 if (exists("filterAcquisitionNumParam")) raw_data <- filterAcquisitionNum(raw_data, filterAcquisitionNumParam[1]:filterAcquisitionNumParam[2]) 80 if (exists("filterAcquisitionNumParam")) raw_data <- filterAcquisitionNum(raw_data, filterAcquisitionNumParam[1]:filterAcquisitionNumParam[2])
79 if (exists("filterRtParam")) raw_data <- filterRt(raw_data, filterRtParam) 81 if (exists("filterRtParam")) raw_data <- filterRt(raw_data, filterRtParam)
80 if (exists("filterMzParam")) raw_data <- filterMz(raw_data, filterMzParam) 82 if (exists("filterMzParam")) raw_data <- filterMz(raw_data, filterMzParam)
81 #Apply this filter only if file contain MS and MSn 83 #Apply this filter only if file contain MS and MSn
82 if(length(unique(msLevel(raw_data)))!= 1){ 84 if (length(unique(msLevel(raw_data))) != 1) {
83 raw_data <- filterMsLevel(raw_data,msLevel=1) 85 raw_data <- filterMsLevel(raw_data, msLevel = 1)
84 } 86 }
85 87
86 cat("\t\t\tChromatographic peak detection\n") 88 cat("\t\t\tChromatographic peak detection\n")
87 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ... 89 # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
88 args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list()))] 90 args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))]
89 91
90 findChromPeaksParam <- do.call(paste0(method,"Param"), args) 92 findChromPeaksParam <- do.call(paste0(method, "Param"), args)
91 print(findChromPeaksParam) 93 print(findChromPeaksParam)
92 xdata <- findChromPeaks(raw_data, param=findChromPeaksParam) 94 xdata <- findChromPeaks(raw_data, param = findChromPeaksParam)
93 95
94 # Check if there are no peaks 96 # Check if there are no peaks
95 if (nrow(chromPeaks(xdata)) == 0) stop("No peaks were detected. You should review your settings") 97 if (nrow(chromPeaks(xdata)) == 0) stop("No peaks were detected. You should review your settings")
96 98
97 # Create a sampleMetada file 99 # Create a sampleMetada file
98 sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv") 100 sampleNamesList <- getSampleMetadata(xdata = xdata, sampleMetadataOutput = "sampleMetadata.tsv")
99
100 #cat("\t\t\tCompute and Store TIC and BPI\n")
101 #chromTIC = chromatogram(xdata, aggregationFun = "sum")
102 #chromBPI = chromatogram(xdata, aggregationFun = "max")
103 101
104 # Create a chromPeaks table if required 102 # Create a chromPeaks table if required
105 if (exists("peaklistParam")) { 103 if (exists("peaklistParam")) {
106 if(peaklistParam){ 104 if (peaklistParam) {
107 cat("\nCreating the chromatographic peaks' table...\n") 105 cat("\nCreating the chromatographic peaks' table...\n")
108 write.table(chromPeaks(xdata), file="chromPeak_table.tsv",sep="\t",quote=F,row.names=F) 106 write.table(chromPeaks(xdata), file = "chromPeak_table.tsv", sep = "\t", quote = F, row.names = F)
109 } 107 }
110 } 108 }
111 109
112 cat("\n\n") 110 cat("\n\n")
113 111
114 # ----- EXPORT ----- 112 # ----- EXPORT -----
122 xset <- getxcmsSetObject(xdata) 120 xset <- getxcmsSetObject(xdata)
123 print(xset) 121 print(xset)
124 cat("\n\n") 122 cat("\n\n")
125 123
126 #saving R data in .Rdata file to save the variables used in the present tool 124 #saving R data in .Rdata file to save the variables used in the present tool
127 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI") 125 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
128 save(list=objects2save[objects2save %in% ls()], file="xcmsSet.RData") 126 save(list = objects2save[objects2save %in% ls()], file = "xcmsSet.RData")
129 127
130 128
131 cat("\tDONE\n") 129 cat("\tDONE\n")