annotate lib.r @ 16:6a4d8753a330 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty
author lecorguille
date Thu, 04 Oct 2018 10:37:03 -0400
parents 833d2c821d9c
children 7a19925478e8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
1 #@authors ABiMS TEAM, Y. Guitton
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
3
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
4 #@author G. Le Corguille
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
5 # solve an issue with batch if arguments are logical TRUE/FALSE
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
6 parseCommandArgs <- function(...) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
7 args <- batch::parseCommandArgs(...)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
8 for (key in names(args)) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
9 if (args[key] %in% c("TRUE","FALSE"))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
10 args[key] = as.logical(args[key])
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
11 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
12 return(args)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
13 }
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
14
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
15 #@author G. Le Corguille
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
16 # This function will
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
17 # - load the packages
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
18 # - display the sessionInfo
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
19 loadAndDisplayPackages <- function(pkgs) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
21
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
22 sessioninfo = sessionInfo()
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
23 cat(sessioninfo$R.version$version.string,"\n")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
24 cat("Main packages:\n")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
26 cat("Other loaded packages:\n")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
28 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
29
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
30 #@author G. Le Corguille
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
31 # This function merge several chromBPI or chromTIC into one.
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
32 mergeChrom <- function(chrom_merged, chrom) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
33 if (is.null(chrom_merged)) return(NULL)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
35 return(chrom_merged)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
36 }
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
37
9
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
38 #@author G. Le Corguille
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
39 # This function merge several xdata into one.
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
40 mergeXData <- function(args) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
41 chromTIC <- NULL
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
42 chromBPI <- NULL
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
43 chromTIC_adjusted <- NULL
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
44 chromBPI_adjusted <- NULL
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
45 for(image in args$images) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
46
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
47 load(image)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
48 # Handle infiles
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
49 if (!exists("singlefile")) singlefile <- NULL
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
50 if (!exists("zipfile")) zipfile <- NULL
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
51 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
52 zipfile <- rawFilePath$zipfile
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
53 singlefile <- rawFilePath$singlefile
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
54 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
55
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
56 if (exists("raw_data")) xdata <- raw_data
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
58
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
59 cat(sampleNamesList$sampleNamesOrigin,"\n")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
60
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
61 if (!exists("xdata_merged")) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
62 xdata_merged <- xdata
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
63 singlefile_merged <- singlefile
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
64 md5sumList_merged <- md5sumList
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
65 sampleNamesList_merged <- sampleNamesList
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
66 chromTIC_merged <- chromTIC
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
67 chromBPI_merged <- chromBPI
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
68 chromTIC_adjusted_merged <- chromTIC_adjusted
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
69 chromBPI_adjusted_merged <- chromBPI_adjusted
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
70 } else {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
74
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
75 singlefile_merged <- c(singlefile_merged,singlefile)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
83 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
84 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
85 rm(image)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
86 xdata <- xdata_merged; rm(xdata_merged)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
87 singlefile <- singlefile_merged; rm(singlefile_merged)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
88 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
90
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
91 if (!is.null(args$sampleMetadata)) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
92 cat("\tXSET PHENODATA SETTING...\n")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
93 sampleMetadataFile <- args$sampleMetadata
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
94 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
95 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
96
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
97 if (any(is.na(pData(xdata)$sample_group))) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
98 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
99 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
100 print(error_message)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
101 stop(error_message)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
102 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
103 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
104
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
105 if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
106 if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
107 if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
108 if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
109
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
110 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
111 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
112
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
113 #@author G. Le Corguille
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
114 # This function convert if it is required the Retention Time in minutes
9
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
115 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
116 if (convertRTMinute){
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
117 #converting the retention times (seconds) into minutes
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
118 print("converting the retention times into minutes in the variableMetadata")
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
119 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
120 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
121 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
9
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
122 }
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
123 return (variableMetadata)
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
124 }
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
125
9
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
126 #@author G. Le Corguille
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
127 # This function format ions identifiers
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
128 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
129 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
130 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
131 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
132 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
133 return(variableMetadata)
9
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
134 }
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
135
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
136 #@author G. Le Corguille
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
137 # This function convert the remain NA to 0 in the dataMatrix
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
138 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
139 if (naTOzero){
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
140 dataMatrix[is.na(dataMatrix)] <- 0
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
141 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
142 return (dataMatrix)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
143 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
144
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
145 #@author G. Le Corguille
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
146 # Draw the plotChromPeakDensity 3 per page in a pdf file
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
147 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
148 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
149
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
150 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
151
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
152 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
153 names(group_colors) <- unique(xdata$sample_group)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
154
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
155 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
156 for (i in 1:nrow(featureDefinitions(xdata))) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
157 mzmin = featureDefinitions(xdata)[i,]$mzmin
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
158 mzmax = featureDefinitions(xdata)[i,]$mzmax
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
159 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
160 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
161 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
162
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
163 dev.off()
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
164 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
165
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
166 #@author G. Le Corguille
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
167 # Draw the plotChromPeakDensity 3 per page in a pdf file
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
168 getPlotAdjustedRtime <- function(xdata) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
169
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
170 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
171
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
172 # Color by group
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
173 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
174 if (length(group_colors) > 1) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
175 names(group_colors) <- unique(xdata$sample_group)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
176 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
177 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
178 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
179
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
180 # Color by sample
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
181 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
182 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
183
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
184 dev.off()
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
185 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
186
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
187 #@author G. Le Corguille
9
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
188 # value: intensity values to be used into, maxo or intb
16
6a4d8753a330 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty
lecorguille
parents: 14
diff changeset
189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
190 dataMatrix <- featureValues(xdata, method="medret", value=intval)
16
6a4d8753a330 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty
lecorguille
parents: 14
diff changeset
191 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
192 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
193 variableMetadata <- featureDefinitions(xdata)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
195 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
196
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
9
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
200
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
201 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
202 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
203
9
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
204 }
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
205
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
206 #@author G. Le Corguille
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
207 # It allow different of field separators
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
208 getDataFrameFromFile <- function(filename, header=T) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
209 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
210 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
211 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
212 if (ncol(myDataFrame) < 2) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
213 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
214 print(error_message)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
215 stop(error_message)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
216 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
217 return(myDataFrame)
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
218 }
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
219
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
220 #@author G. Le Corguille
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
221 # Draw the BPI and TIC graphics
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
222 # colored by sample names or class names
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
223 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
224
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
225 if (aggregationFun == "sum")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
226 type="Total Ion Chromatograms"
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
227 else
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
228 type="Base Peak Intensity Chromatograms"
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
229
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
230 adjusted="Raw"
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
231 if (hasAdjustedRtime(xdata))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
232 adjusted="Adjusted"
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
233
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
234 main <- paste(type,":",adjusted,"data")
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
235
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
236 pdf(pdfname, width=16, height=10)
9
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
237
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
238 # Color by group
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
239 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
240 if (length(group_colors) > 1) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
241 names(group_colors) <- unique(xdata$sample_group)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
242 plot(chrom, col = group_colors[chrom$sample_group], main=main)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
243 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
244 }
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
245
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
246 # Color by sample
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
247 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
248 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
249
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
250 dev.off()
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
251 }
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
252
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
253
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
254 # Get the polarities from all the samples of a condition
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
255 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
256 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
257 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
258 cat("Creating the sampleMetadata file...\n")
9
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
259
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
260 #Create the sampleMetada dataframe
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
261 sampleMetadata <- xdata@phenoData@data
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
262 rownames(sampleMetadata) <- NULL
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
263 colnames(sampleMetadata) <- c("sampleMetadata", "class")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
264
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
265 sampleNamesOrigin <- sampleMetadata$sampleMetadata
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
266 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
267
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
268 if (any(duplicated(sampleNamesMakeNames))) {
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
269 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
270 for (sampleName in sampleNamesOrigin) {
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
271 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
272 }
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
273 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
274 }
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
275
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
276 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
277 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
278 for (sampleName in sampleNamesOrigin) {
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
279 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
280 }
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
281 }
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
282
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
283 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
284
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
285
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
286 #For each sample file, the following actions are done
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
287 for (fileIdx in 1:length(fileNames(xdata))) {
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
288 #Check if the file is in the CDF format
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
289 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
290
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
291 # If the column isn't exist, with add one filled with NA
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
292 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
293
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
294 #Extract the polarity (a list of polarities)
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
295 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
296 #Verify if all the scans have the same polarity
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
297 uniq_list <- unique(polarity)
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
298 if (length(uniq_list)>1){
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
299 polarity <- "mixed"
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
300 } else {
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
301 polarity <- as.character(uniq_list)
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
302 }
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
303
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
304 #Set the polarity attribute
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
305 sampleMetadata$polarity[fileIdx] <- polarity
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
306 }
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
307
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
308 }
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
309
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
310 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
311
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
312 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
313
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
314 }
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
315
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
316
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
317 # This function check if xcms will found all the files
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
318 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
319 checkFilesCompatibilityWithXcms <- function(directory) {
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
320 cat("Checking files filenames compatibilities with xmcs...\n")
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
321 # WHAT XCMS WILL FIND
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
322 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
323 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
324 info <- file.info(directory)
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
325 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
326 files <- c(directory[!info$isdir], listed)
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
327 files_abs <- file.path(getwd(), files)
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
328 exists <- file.exists(files_abs)
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
329 files[exists] <- files_abs[exists]
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
330 files[exists] <- sub("//","/",files[exists])
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
331
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
332 # WHAT IS ON THE FILESYSTEM
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
333 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
334 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
335
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
336 # COMPARISON
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
337 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
338 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
339 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
340 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
341 }
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
342 }
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
343
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
344
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
345 #This function list the compatible files within the directory as xcms did
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
346 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
347 getMSFiles <- function (directory) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
348 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
349 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
350 info <- file.info(directory)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
351 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
352 files <- c(directory[!info$isdir], listed)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
353 exists <- file.exists(files)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
354 files <- files[exists]
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
355 return(files)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
356 }
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
357
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
358 # This function check if XML contains special caracters. It also checks integrity and completness.
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
359 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
360 checkXmlStructure <- function (directory) {
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
361 cat("Checking XML structure...\n")
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
362
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
363 cmd <- paste0("IFS=$'\n'; for xml in $(find '",directory,"' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
364 capture <- system(cmd, intern=TRUE)
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
365
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
366 if (length(capture)>0){
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
367 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
368 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
369 write(capture, stderr())
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
370 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
371 }
9
2c1d7df89cf6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 4
diff changeset
372
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
373 }
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
374
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
375
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
376 # This function check if XML contain special characters
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
377 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
378 deleteXmlBadCharacters<- function (directory) {
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
379 cat("Checking Non ASCII characters in the XML...\n")
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
380
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
381 processed <- F
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
382 l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE)
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
383 for (i in l){
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
384 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
385 capture <- suppressWarnings(system(cmd, intern=TRUE))
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
386 if (length(capture)>0){
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
387 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
388 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
389 c <- system(cmd, intern=TRUE)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
390 capture <- ""
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
391 processed <- T
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
392 }
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
393 }
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
394 if (processed) cat("\n\n")
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
395 return(processed)
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
396 }
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
397
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
398
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
399 # This function will compute MD5 checksum to check the data integrity
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
400 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
401 getMd5sum <- function (directory) {
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
402 cat("Compute md5 checksum...\n")
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
403 # WHAT XCMS WILL FIND
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
404 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
405 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|")
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
406 info <- file.info(directory)
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
407 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
408 files <- c(directory[!info$isdir], listed)
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
409 exists <- file.exists(files)
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
410 files <- files[exists]
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
411
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
412 library(tools)
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
413
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
414 #cat("\n\n")
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
415
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
416 return(as.matrix(md5sum(files)))
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
417 }
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
418
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
419
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
420 # This function get the raw file path from the arguments
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
421 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
422 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
423 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
424
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
425 if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]]
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
426
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
427 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
428 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]]
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
429 singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]]
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
430 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
431 if (exists("singlefile_galaxyPaths")){
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
432 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|"))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
433 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|"))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
434
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
435 singlefile <- NULL
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
436 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
437 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
438 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
439 # In case, an url is used to import data within Galaxy
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
440 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
441 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
442 }
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
443 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
444 return(list(zipfile=zipfile, singlefile=singlefile))
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
445 }
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
446
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
447 # This function retrieve the raw file in the working directory
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
448 # - if zipfile: unzip the file with its directory tree
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
449 # - if singlefiles: set symlink with the good filename
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
450 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
451 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
452 if(!is.null(singlefile) && (length("singlefile")>0)) {
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
453 for (singlefile_sampleName in names(singlefile)) {
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
454 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
455 if(!file.exists(singlefile_galaxyPath)){
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
456 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
457 print(error_message); stop(error_message)
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
458 }
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
459
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
460 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
461 file.copy(singlefile_galaxyPath, singlefile_sampleName)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
462
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
463 }
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
464 directory <- "."
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
465
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
466 }
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
467 if(!is.null(zipfile) && (zipfile != "")) {
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
468 if(!file.exists(zipfile)){
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
469 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
470 print(error_message)
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
471 stop(error_message)
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
472 }
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
473
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
474 #list all file in the zip file
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
475 #zip_files <- unzip(zipfile,list=T)[,"Name"]
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
476
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
477 #unzip
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
478 suppressWarnings(unzip(zipfile, unzip="unzip"))
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
479
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
480 #get the directory name
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
481 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
482 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
483 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
484 directory <- "."
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
485 if (length(directories) == 1) directory <- directories
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
486
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
487 cat("files_root_directory\t",directory,"\n")
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
488
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
489 }
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 9
diff changeset
490 return (directory)
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
diff changeset
491 }
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
492
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
493
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
494 # This function retrieve a xset like object
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
495 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
496 getxcmsSetObject <- function(xobject) {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
497 # XCMS 1.x
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
498 if (class(xobject) == "xcmsSet")
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
499 return (xobject)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
500 # XCMS 3.x
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
501 if (class(xobject) == "XCMSnExp") {
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
502 # Get the legacy xcmsSet object
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
503 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
504 if (!is.null(xset@phenoData$sample_group))
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
505 sampclass(xset) <- xset@phenoData$sample_group
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
506 else
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
507 sampclass(xset) <- "."
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
508 return (xset)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
509 }
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 10
diff changeset
510 }