Mercurial > repos > lecorguille > msnbase_readmsdata

annotate lib.r @ 15:b25a582ab6c1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author workflow4metabolomics
date Mon, 15 Jul 2024 15:56:53 +0000
parents cdebdb178031
children 733d32b30aff
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
1 #@authors ABiMS TEAM, Y. Guitton
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
3
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
4 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
5 # solve an issue with batch if arguments are logical TRUE/FALSE
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
6 parseCommandArgs <- function(...) {
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
7 args <- batch::parseCommandArgs(...)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
8 for (key in names(args)) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
9 if (args[key] %in% c("TRUE", "FALSE"))
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
10 args[key] <- as.logical(args[key])
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
11 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
12 return(args)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
13 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
14
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
15 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
16 # This function will
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
17 # - load the packages
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
18 # - display the sessionInfo
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
19 loadAndDisplayPackages <- function(pkgs) {
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
20 for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
21
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
22 sessioninfo <- sessionInfo()
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
23 cat(sessioninfo$R.version$version.string, "\n")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
24 cat("Main packages:\n")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
25 for (pkg in names(sessioninfo$otherPkgs)) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
26 cat(paste(pkg, packageVersion(pkg)), "\t")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
27 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
28 cat("\n")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
29 cat("Other loaded packages:\n")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
30 for (pkg in names(sessioninfo$loadedOnly)) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
31 cat(paste(pkg, packageVersion(pkg)), "\t")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
32 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
33 cat("\n")
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
34 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
35
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
36 #@author G. Le Corguille
2
fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
parents: 0
diff changeset
37 # This function merge several chromBPI or chromTIC into one.
4
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 3
diff changeset
38 mergeChrom <- function(chrom_merged, chrom) {
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
39 if (is.null(chrom_merged)) return(NULL)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
40 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
41 return(chrom_merged)
2
fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
parents: 0
diff changeset
42 }
fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
parents: 0
diff changeset
43
fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty
lecorguille
parents: 0
diff changeset
44 #@author G. Le Corguille
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
45 # This function merge several xdata into one.
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
46 mergeXData <- function(args) {
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
47 chromTIC <- NULL
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
48 chromBPI <- NULL
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
49 chromTIC_adjusted <- NULL
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
50 chromBPI_adjusted <- NULL
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
51 md5sumList <- NULL
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
52 for (image in args$images) {
4
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 3
diff changeset
53
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
54 load(image)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
55 # Handle infiles
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
56 if (!exists("singlefile")) singlefile <- NULL
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
57 if (!exists("zipfile")) zipfile <- NULL
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
58 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
59 zipfile <- rawFilePath$zipfile
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
60 singlefile <- rawFilePath$singlefile
4
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 3
diff changeset
61
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
62 if (exists("raw_data")) xdata <- raw_data
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
63 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
4
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 3
diff changeset
64
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
65 cat(sampleNamesList$sampleNamesOrigin, "\n")
4
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 3
diff changeset
66
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
67 if (!exists("xdata_merged")) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
68 xdata_merged <- xdata
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
69 singlefile_merged <- singlefile
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
70 md5sumList_merged <- md5sumList
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
71 sampleNamesList_merged <- sampleNamesList
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
72 chromTIC_merged <- chromTIC
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
73 chromBPI_merged <- chromBPI
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
74 chromTIC_adjusted_merged <- chromTIC_adjusted
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
75 chromBPI_adjusted_merged <- chromBPI_adjusted
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
76 } else {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
77 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged, xdata)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
78 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged, xdata)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
79 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
4
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 3
diff changeset
80
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
81 singlefile_merged <- c(singlefile_merged, singlefile)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
82 md5sumList_merged$origin <- rbind(md5sumList_merged$origin, md5sumList$origin)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
83 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin, sampleNamesList$sampleNamesOrigin)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
84 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames, sampleNamesList$sampleNamesMakeNames)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
85 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
86 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
87 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
88 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
89 }
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
90 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
91 rm(image)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
92 xdata <- xdata_merged
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
93 rm(xdata_merged)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
94 singlefile <- singlefile_merged
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
95 rm(singlefile_merged)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
96 md5sumList <- md5sumList_merged
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
97 rm(md5sumList_merged)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
98 sampleNamesList <- sampleNamesList_merged
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
99 rm(sampleNamesList_merged)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
100
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
101 if (!is.null(args$sampleMetadata)) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
102 cat("\tXSET PHENODATA SETTING...\n")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
103 sampleMetadataFile <- args$sampleMetadata
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
104 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header = FALSE)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
105 xdata@phenoData@data$sample_group <- sampleMetadata$V2[match(xdata@phenoData@data$sample_name, sampleMetadata$V1)]
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
106
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
107 if (any(is.na(pData(xdata)$sample_group))) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
108 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
109 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse = " "))
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
110 print(error_message)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
111 stop(error_message)
14
cdebdb178031 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
workflow4metabolomics
parents: 13
diff changeset
112 }
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
113 }
4
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 3
diff changeset
114
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
115 if (!is.null(chromTIC_merged)) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
116 chromTIC <- chromTIC_merged
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
117 chromTIC@phenoData <- xdata@phenoData
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
118 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
119 if (!is.null(chromBPI_merged)) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
120 chromBPI <- chromBPI_merged
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
121 chromBPI@phenoData <- xdata@phenoData
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
122 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
123 if (!is.null(chromTIC_adjusted_merged)) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
124 chromTIC_adjusted <- chromTIC_adjusted_merged
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
125 chromTIC_adjusted@phenoData <- xdata@phenoData
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
126 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
127 if (!is.null(chromBPI_adjusted_merged)) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
128 chromBPI_adjusted <- chromBPI_adjusted_merged
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
129 chromBPI_adjusted@phenoData <- xdata@phenoData
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
130 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
131
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
132 return(list("xdata" = xdata, "singlefile" = singlefile, "md5sumList" = md5sumList, "sampleNamesList" = sampleNamesList, "chromTIC" = chromTIC, "chromBPI" = chromBPI, "chromTIC_adjusted" = chromTIC_adjusted, "chromBPI_adjusted" = chromBPI_adjusted))
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
133 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
134
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
135 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
136 # This function convert if it is required the Retention Time in minutes
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
137 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
138 if (convertRTMinute) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
139 #converting the retention times (seconds) into minutes
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
140 print("converting the retention times into minutes in the variableMetadata")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
141 variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
142 variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
143 variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
144 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
145 return(variableMetadata)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
146 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
147
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
148 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
149 # This function format ions identifiers
14
cdebdb178031 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
workflow4metabolomics
parents: 13
diff changeset
150 formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
151 splitDeco <- strsplit(as.character(variableMetadata$name), "_")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
152 idsDeco <- sapply(splitDeco,
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
153 function(x) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
154 deco <- unlist(x)[2]
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
155 if (is.na(deco)) return("") else return(paste0("_", deco))
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
156 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
157 )
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
158 namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
159 variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
160 return(variableMetadata)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
161 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
162
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
163 #@author G. Le Corguille
5
8705b9de3e6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 4
diff changeset
164 # This function convert the remain NA to 0 in the dataMatrix
8705b9de3e6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 4
diff changeset
165 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
166 if (naTOzero) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
167 dataMatrix[is.na(dataMatrix)] <- 0
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
168 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
169 return(dataMatrix)
5
8705b9de3e6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 4
diff changeset
170 }
8705b9de3e6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 4
diff changeset
171
8705b9de3e6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
parents: 4
diff changeset
172 #@author G. Le Corguille
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
173 # Draw the plotChromPeakDensity 3 per page in a pdf file
14
cdebdb178031 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
workflow4metabolomics
parents: 13
diff changeset
174 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit = 4) {
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
175 pdf(file = "plotChromPeakDensity.pdf", width = 16, height = 12)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
176
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
177 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
178
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
179 if (length(unique(xdata$sample_group)) < 10) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
180 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
181 } else {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
182 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
183 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
184 names(group_colors) <- unique(xdata$sample_group)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
185 col_per_samp <- as.character(xdata$sample_group)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
186 for (i in seq_len(length(group_colors))) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
187 col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i]
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
188 }
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
189
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
190 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
191 for (i in seq_len(nrow(featureDefinitions(xdata)))) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
192 mzmin <- featureDefinitions(xdata)[i, ]$mzmin
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
193 mzmax <- featureDefinitions(xdata)[i, ]$mzmax
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
194 plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, pch = 16, xlim = xlim, main = paste(round(mzmin, mzdigit), round(mzmax, mzdigit)))
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
195 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
196 }
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
197
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
198 dev.off()
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
199 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
200
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
201 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
202 # Draw the plotChromPeakDensity 3 per page in a pdf file
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
203 getPlotAdjustedRtime <- function(xdata) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
204
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
205 pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
206
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
207 # Color by group
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
208 if (length(unique(xdata$sample_group)) < 10) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
209 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
210 } else {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
211 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
212 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
213 if (length(group_colors) > 1) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
214 names(group_colors) <- unique(xdata$sample_group)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
215 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
216 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
217 }
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
218
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
219 # Color by sample
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
220 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
221 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
222
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
223 dev.off()
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
224 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
225
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
226 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
227 # value: intensity values to be used into, maxo or intb
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
228 getPeaklistW4M <- function(xdata, intval = "into", convertRTMinute = FALSE, numDigitsMZ = 4, numDigitsRT = 0, naTOzero = TRUE, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
229 dataMatrix <- featureValues(xdata, method = "medret", value = intval)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
230 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
231 dataMatrix <- cbind(name = groupnames(xdata), dataMatrix)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
232 variableMetadata <- featureDefinitions(xdata)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
233 colnames(variableMetadata)[1] <- "mz"
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
234 colnames(variableMetadata)[4] <- "rt"
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
235 variableMetadata <- data.frame(name = groupnames(xdata), variableMetadata)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
236
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
237 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
238 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
239 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
240
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
241 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
242 variableMetadata[, "peakidx"] <- vapply(variableMetadata[, "peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
8
74bc549b989d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
lecorguille
parents: 7
diff changeset
243
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
244 write.table(variableMetadata, file = variableMetadataOutput, sep = "\t", quote = FALSE, row.names = FALSE)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
245 write.table(dataMatrix, file = dataMatrixOutput, sep = "\t", quote = FALSE, row.names = FALSE)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
246
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
247 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
248
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
249 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
250 # It allow different of field separators
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
251 getDataFrameFromFile <- function(filename, header = TRUE) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
252 myDataFrame <- read.table(filename, header = header, sep = ";", stringsAsFactors = FALSE)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
253 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = "\t", stringsAsFactors = FALSE)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
254 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = ",", stringsAsFactors = FALSE)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
255 if (ncol(myDataFrame) < 2) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
256 error_message <- "Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
257 print(error_message)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
258 stop(error_message)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
259 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
260 return(myDataFrame)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
261 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
262
4
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 3
diff changeset
263 #@author G. Le Corguille
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 3
diff changeset
264 # Draw the BPI and TIC graphics
df53d666da13 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 088699d00f7e45bebb7da07bebc005c68df058d8
lecorguille
parents: 3
diff changeset
265 # colored by sample names or class names
14
cdebdb178031 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
workflow4metabolomics
parents: 13
diff changeset
266 getPlotChromatogram <- function(chrom, xdata, pdfname = "Chromatogram.pdf", aggregationFun = "max") {
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
267
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
268 if (aggregationFun == "sum")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
269 type <- "Total Ion Chromatograms"
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
270 else
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
271 type <- "Base Peak Intensity Chromatograms"
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
272
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
273 adjusted <- "Raw"
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
274 if (hasAdjustedRtime(xdata))
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
275 adjusted <- "Adjusted"
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
276
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
277 main <- paste(type, ":", adjusted, "data")
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
278
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
279 pdf(pdfname, width = 16, height = 10)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
280
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
281 # Color by group
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
282 if (length(unique(xdata$sample_group)) < 10) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
283 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
284 } else {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
285 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
286 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
287 if (length(group_colors) > 1) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
288 names(group_colors) <- unique(xdata$sample_group)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
289 plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
290 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
291 }
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
292
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
293 # Color by sample
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
294 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main = main, peakType = "none")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
295 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
296
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
297 dev.off()
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
298 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
299
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
300
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
301 # Get the polarities from all the samples of a condition
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
302 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
303 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
14
cdebdb178031 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
workflow4metabolomics
parents: 13
diff changeset
304 getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
305 cat("Creating the sampleMetadata file...\n")
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
306
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
307 #Create the sampleMetada dataframe
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
308 sampleMetadata <- xdata@phenoData@data
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
309 rownames(sampleMetadata) <- NULL
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
310 colnames(sampleMetadata) <- c("sample_name", "class")
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
311
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
312 sampleNamesOrigin <- sampleMetadata$sample_name
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
313 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
314
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
315 if (any(duplicated(sampleNamesMakeNames))) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
316 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())
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
317 for (sampleName in sampleNamesOrigin) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
318 write(paste(sampleName, "\t->\t", make.names(sampleName)), stderr())
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
319 }
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
320 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
321 }
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
322
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
323 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
324 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")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
325 for (sampleName in sampleNamesOrigin) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
326 cat(paste(sampleName, "\t->\t", make.names(sampleName), "\n"))
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
327 }
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
328 }
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
329
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
330 sampleMetadata$sample_name <- sampleNamesMakeNames
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
331
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
332
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
333 #For each sample file, the following actions are done
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
334 for (fileIdx in seq_len(length(fileNames(xdata)))) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
335 #Check if the file is in the CDF format
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
336 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
337
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
338 # If the column isn't exist, with add one filled with NA
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
339 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
340
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
341 #Extract the polarity (a list of polarities)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
342 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"]
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
343 #Verify if all the scans have the same polarity
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
344 uniq_list <- unique(polarity)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
345 if (length(uniq_list) > 1) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
346 polarity <- "mixed"
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
347 } else {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
348 polarity <- as.character(uniq_list)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
349 }
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
350
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
351 #Set the polarity attribute
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
352 sampleMetadata$polarity[fileIdx] <- polarity
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
353 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
354
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
355 }
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
356
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
357 write.table(sampleMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = sampleMetadataOutput)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
358
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
359 return(list("sampleNamesOrigin" = sampleNamesOrigin, "sampleNamesMakeNames" = sampleNamesMakeNames))
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
360
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
361 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
362
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
363
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
364 # This function will compute MD5 checksum to check the data integrity
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
365 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
14
cdebdb178031 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
workflow4metabolomics
parents: 13
diff changeset
366 getMd5sum <- function(files) {
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
367 cat("Compute md5 checksum...\n")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
368 library(tools)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
369 return(as.matrix(md5sum(files)))
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
370 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
371
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
372 # This function retrieve the raw file in the working directory
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
373 # - if zipfile: unzip the file with its directory tree
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
374 # - if singlefiles: set symlink with the good filename
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
375 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
14
cdebdb178031 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
workflow4metabolomics
parents: 13
diff changeset
376 retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") {
13
cda005bc221c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 10
diff changeset
377
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
378 if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
13
cda005bc221c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 10
diff changeset
379
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
380 # single - if the file are passed in the command arguments -> refresh singlefile
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
381 if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
382 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\|"))
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
383 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\|"))
13
cda005bc221c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 10
diff changeset
384
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
385 singlefile <- NULL
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
386 for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
387 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
388 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
389 # In case, an url is used to import data within Galaxy
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
390 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName, "/")), n = 1)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
391 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
392 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
393 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
394 # zipfile - if the file are passed in the command arguments -> refresh zipfile
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
395 if (!is.null(args[[paste0("zipfile", prefix)]]))
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
396 zipfile <- args[[paste0("zipfile", prefix)]]
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
397
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
398 # single
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
399 if (!is.null(singlefile) && (length("singlefile") > 0)) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
400 files <- vector()
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
401 for (singlefile_sampleName in names(singlefile)) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
402 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
403 if (!file.exists(singlefile_galaxyPath)) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
404 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
405 print(error_message)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
406 stop(error_message)
13
cda005bc221c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 10
diff changeset
407 }
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
408
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
409 if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = TRUE)))
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
410 file.copy(singlefile_galaxyPath, singlefile_sampleName)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
411 files <- c(files, singlefile_sampleName)
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
412 }
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
413 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
414 # zipfile
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
415 if (!is.null(zipfile) && (zipfile != "")) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
416 if (!file.exists(zipfile)) {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
417 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
418 print(error_message)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
419 stop(error_message)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
420 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
421 suppressWarnings(unzip(zipfile, unzip = "unzip"))
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
422
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
423 #get the directory name
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
424 suppressWarnings(filesInZip <- unzip(zipfile, list = TRUE))
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
425 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
426 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
427 directory <- "."
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
428 if (length(directories) == 1) directory <- directories
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
429
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
430 cat("files_root_directory\t", directory, "\n")
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
431
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
432 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
433 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
434 info <- file.info(directory)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
435 listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
436 files <- c(directory[!info$isdir], listed)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
437 exists <- file.exists(files)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
438 files <- files[exists]
13
cda005bc221c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 10
diff changeset
439
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
440 }
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
441 return(list(zipfile = zipfile, singlefile = singlefile, files = files))
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
442 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
443
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
444
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
445 # This function retrieve a xset like object
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
446 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
447 getxcmsSetObject <- function(xobject) {
15
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
448 # XCMS 1.x
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
449 if (class(xobject) == "xcmsSet")
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
450 return(xobject)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
451 # XCMS 3.x
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
452 if (class(xobject) == "XCMSnExp") {
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
453 # Get the legacy xcmsSet object
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
454 suppressWarnings(xset <- as(xobject, "xcmsSet"))
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
455 if (!is.null(xset@phenoData$sample_group))
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
456 sampclass(xset) <- xset@phenoData$sample_group
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
457 else
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
458 sampclass(xset) <- "."
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
459 return(xset)
b25a582ab6c1 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents: 14
diff changeset
460 }
0
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty
lecorguille
parents:
diff changeset
461 }