Mercurial > repos > workflow4metabolomics > xcms_refine

annotate lib.r @ 3:6c2798bce3eb draft default tip

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 95721ced8347c09e79340e6d67ecb41c5cc64163
author workflow4metabolomics
date Mon, 03 Feb 2025 14:46:55 +0000
parents 20f8ebc3a391
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
1 # @authors ABiMS TEAM, Y. Guitton
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
3
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
4 # @author G. Le Corguille
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
5 # solve an issue with batch if arguments are logical TRUE/FALSE
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
6 parseCommandArgs <- function(...) {
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
7 args <- batch::parseCommandArgs(...)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
8 for (key in names(args)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
9 if (args[key] %in% c("TRUE", "FALSE")) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
10 args[key] <- as.logical(args[key])
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
11 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
12 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
13 return(args)
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
14 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
15
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
16 # @author G. Le Corguille
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
17 # This function will
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
18 # - load the packages
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
19 # - display the sessionInfo
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
20 loadAndDisplayPackages <- function(pkgs) {
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
21 for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
22
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
23 sessioninfo <- sessionInfo()
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
24 cat(sessioninfo$R.version$version.string, "\n")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
25 cat("Main packages:\n")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
26 for (pkg in names(sessioninfo$otherPkgs)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
27 cat(paste(pkg, packageVersion(pkg)), "\t")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
28 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
29 cat("\n")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
30 cat("Other loaded packages:\n")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
31 for (pkg in names(sessioninfo$loadedOnly)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
32 cat(paste(pkg, packageVersion(pkg)), "\t")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
33 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
34 cat("\n")
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
35 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
36
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
37 # @author G. Le Corguille
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
38 # This function merge several chromBPI or chromTIC into one.
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
39 mergeChrom <- function(chrom_merged, chrom) {
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
40 if (is.null(chrom_merged)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
41 return(NULL)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
42 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
43 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
44 return(chrom_merged)
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
45 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
46
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
47 # @author G. Le Corguille
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
48 # This function merge several xdata into one.
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
49 mergeXData <- function(args) {
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
50 chromTIC <- NULL
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
51 chromBPI <- NULL
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
52 chromTIC_adjusted <- NULL
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
53 chromBPI_adjusted <- NULL
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
54 md5sumList <- NULL
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
55 for (image in args$images) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
56 load(image)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
57 # Handle infiles
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
58 if (!exists("singlefile")) singlefile <- NULL
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
59 if (!exists("zipfile")) zipfile <- NULL
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
60 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
61 zipfile <- rawFilePath$zipfile
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
62 singlefile <- rawFilePath$singlefile
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
63
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
64 if (exists("raw_data")) xdata <- raw_data
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
65 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
66
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
67 cat(sampleNamesList$sampleNamesOrigin, "\n")
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
68
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
69 if (!exists("xdata_merged")) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
70 xdata_merged <- xdata
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
71 singlefile_merged <- singlefile
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
72 md5sumList_merged <- md5sumList
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
73 sampleNamesList_merged <- sampleNamesList
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
74 chromTIC_merged <- chromTIC
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
75 chromBPI_merged <- chromBPI
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
76 chromTIC_adjusted_merged <- chromTIC_adjusted
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
77 chromBPI_adjusted_merged <- chromBPI_adjusted
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
78 } else {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
79 if (is(xdata, "XCMSnExp")) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
80 xdata_merged <- c(xdata_merged, xdata)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
81 } else if (is(xdata, "OnDiskMSnExp")) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
82 xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged, xdata)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
83 } else {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
84 stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
85 }
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
86
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
87 singlefile_merged <- c(singlefile_merged, singlefile)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
88 md5sumList_merged$origin <- rbind(md5sumList_merged$origin, md5sumList$origin)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
89 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin, sampleNamesList$sampleNamesOrigin)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
90 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames, sampleNamesList$sampleNamesMakeNames)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
91 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
92 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
93 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
94 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
95 }
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
96 }
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
97 rm(image)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
98 xdata <- xdata_merged
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
99 rm(xdata_merged)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
100 singlefile <- singlefile_merged
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
101 rm(singlefile_merged)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
102 md5sumList <- md5sumList_merged
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
103 rm(md5sumList_merged)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
104 sampleNamesList <- sampleNamesList_merged
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
105 rm(sampleNamesList_merged)
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
106
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
107 if (!is.null(args$sampleMetadata)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
108 cat("\tXSET PHENODATA SETTING...\n")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
109 sampleMetadataFile <- args$sampleMetadata
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
110 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header = FALSE)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
111 xdata@phenoData@data$sample_group <- sampleMetadata$V2[match(xdata@phenoData@data$sample_name, sampleMetadata$V1)]
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
112
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
113 if (any(is.na(pData(xdata)$sample_group))) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
114 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
115 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse = " "))
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
116 print(error_message)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
117 stop(error_message)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
118 }
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
119 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
120
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
121 if (!is.null(chromTIC_merged)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
122 chromTIC <- chromTIC_merged
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
123 chromTIC@phenoData <- xdata@phenoData
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
124 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
125 if (!is.null(chromBPI_merged)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
126 chromBPI <- chromBPI_merged
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
127 chromBPI@phenoData <- xdata@phenoData
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
128 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
129 if (!is.null(chromTIC_adjusted_merged)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
130 chromTIC_adjusted <- chromTIC_adjusted_merged
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
131 chromTIC_adjusted@phenoData <- xdata@phenoData
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
132 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
133 if (!is.null(chromBPI_adjusted_merged)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
134 chromBPI_adjusted <- chromBPI_adjusted_merged
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
135 chromBPI_adjusted@phenoData <- xdata@phenoData
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
136 }
1
20f8ebc3a391 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
workflow4metabolomics
parents: 0
diff changeset
137
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
138 return(list("xdata" = xdata, "singlefile" = singlefile, "md5sumList" = md5sumList, "sampleNamesList" = sampleNamesList, "chromTIC" = chromTIC, "chromBPI" = chromBPI, "chromTIC_adjusted" = chromTIC_adjusted, "chromBPI_adjusted" = chromBPI_adjusted))
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
139 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
140
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
141 # @author G. Le Corguille
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
142 # This function convert if it is required the Retention Time in minutes
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
143 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
144 if (convertRTMinute) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
145 # converting the retention times (seconds) into minutes
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
146 print("converting the retention times into minutes in the variableMetadata")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
147 variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
148 variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
149 variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
150 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
151 return(variableMetadata)
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
152 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
153
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
154 # @author G. Le Corguille
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
155 # This function format ions identifiers
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
156 formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
157 splitDeco <- strsplit(as.character(variableMetadata$name), "_")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
158 idsDeco <- sapply(
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
159 splitDeco,
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
160 function(x) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
161 deco <- unlist(x)[2]
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
162 if (is.na(deco)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
163 return("")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
164 } else {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
165 return(paste0("_", deco))
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
166 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
167 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
168 )
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
169 namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
170 variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
171 return(variableMetadata)
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
172 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
173
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
174 # @author G. Le Corguille
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
175 # This function convert the remain NA to 0 in the dataMatrix
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
176 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
177 if (naTOzero) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
178 dataMatrix[is.na(dataMatrix)] <- 0
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
179 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
180 return(dataMatrix)
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
181 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
182
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
183 # @author G. Le Corguille
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
184 # Draw the plotChromPeakDensity 3 per page in a pdf file
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
185 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit = 4) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
186 pdf(file = "plotChromPeakDensity.pdf", width = 16, height = 12)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
187
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
188 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
189
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
190 if (length(unique(xdata$sample_group)) < 10) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
191 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
192 } else {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
193 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
194 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
195 names(group_colors) <- unique(xdata$sample_group)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
196 col_per_samp <- as.character(xdata$sample_group)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
197 for (i in seq_len(length(group_colors))) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
198 col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i]
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
199 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
200
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
201 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
202 for (i in seq_len(nrow(featureDefinitions(xdata)))) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
203 mzmin <- featureDefinitions(xdata)[i, ]$mzmin
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
204 mzmax <- featureDefinitions(xdata)[i, ]$mzmax
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
205 plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, pch = 16, xlim = xlim, main = paste(round(mzmin, mzdigit), round(mzmax, mzdigit)))
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
206 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
207 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
208
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
209 dev.off()
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
210 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
211
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
212 # @author G. Le Corguille
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
213 # Draw the plotChromPeakDensity 3 per page in a pdf file
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
214 getPlotAdjustedRtime <- function(xdata) {
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
215 pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12)
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
216
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
217 # Color by group
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
218 if (length(unique(xdata$sample_group)) < 10) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
219 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
220 } else {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
221 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
222 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
223 if (length(group_colors) > 1) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
224 names(group_colors) <- unique(xdata$sample_group)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
225 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
226 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
227 }
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
228
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
229 # Color by sample
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
230 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
231 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
232
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
233 dev.off()
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
234 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
235
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
236 # @author G. Le Corguille
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
237 # value: intensity values to be used into, maxo or intb
1
20f8ebc3a391 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
workflow4metabolomics
parents: 0
diff changeset
238 getPeaklistW4M <- function(xdata, intval = "into", convertRTMinute = FALSE, numDigitsMZ = 4, numDigitsRT = 0, naTOzero = TRUE, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
239 dataMatrix <- featureValues(xdata, method = "medret", value = intval)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
240 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
241 dataMatrix <- cbind(name = groupnames(xdata), dataMatrix)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
242 variableMetadata <- featureDefinitions(xdata)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
243 colnames(variableMetadata)[1] <- "mz"
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
244 colnames(variableMetadata)[4] <- "rt"
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
245 variableMetadata <- data.frame(name = groupnames(xdata), variableMetadata)
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
246
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
247 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
248 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
249 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
250
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
251 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
252 variableMetadata[, "peakidx"] <- vapply(variableMetadata[, "peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
253
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
254 write.table(variableMetadata, file = variableMetadataOutput, sep = "\t", quote = FALSE, row.names = FALSE)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
255 write.table(dataMatrix, file = dataMatrixOutput, sep = "\t", quote = FALSE, row.names = FALSE)
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
256 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
257
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
258 # @author G. Le Corguille
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
259 # It allow different of field separators
1
20f8ebc3a391 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
workflow4metabolomics
parents: 0
diff changeset
260 getDataFrameFromFile <- function(filename, header = TRUE) {
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
261 myDataFrame <- read.table(filename, header = header, sep = ";", stringsAsFactors = FALSE)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
262 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = "\t", stringsAsFactors = FALSE)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
263 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header = header, sep = ",", stringsAsFactors = FALSE)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
264 if (ncol(myDataFrame) < 2) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
265 error_message <- "Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
266 print(error_message)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
267 stop(error_message)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
268 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
269 return(myDataFrame)
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
270 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
271
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
272 # @author G. Le Corguille
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
273 # Draw the BPI and TIC graphics
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
274 # colored by sample names or class names
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
275 getPlotChromatogram <- function(chrom, xdata, pdfname = "Chromatogram.pdf", aggregationFun = "max") {
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
276 if (aggregationFun == "sum") {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
277 type <- "Total Ion Chromatograms"
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
278 } else {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
279 type <- "Base Peak Intensity Chromatograms"
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
280 }
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
281
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
282 adjusted <- "Raw"
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
283 if (hasAdjustedRtime(xdata)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
284 adjusted <- "Adjusted"
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
285 }
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
286
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
287 main <- paste(type, ":", adjusted, "data")
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
288
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
289 pdf(pdfname, width = 16, height = 10)
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
290
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
291 # Color by group
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
292 if (length(unique(xdata$sample_group)) < 10) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
293 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
294 } else {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
295 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
296 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
297 if (length(group_colors) > 1) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
298 names(group_colors) <- unique(xdata$sample_group)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
299 plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
300 legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
301 }
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
302
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
303 # Color by sample
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
304 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main = main, peakType = "none")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
305 legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
306
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
307 dev.off()
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
308 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
309
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
310
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
311 # Get the polarities from all the samples of a condition
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
312 # @author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
313 # @author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
314 getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
315 cat("Creating the sampleMetadata file...\n")
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
316
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
317 # Create the sampleMetada dataframe
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
318 sampleMetadata <- xdata@phenoData@data
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
319 rownames(sampleMetadata) <- NULL
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
320 colnames(sampleMetadata) <- c("sample_name", "class")
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
321
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
322 sampleNamesOrigin <- sampleMetadata$sample_name
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
323 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
324
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
325 if (any(duplicated(sampleNamesMakeNames))) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
326 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())
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
327 for (sampleName in sampleNamesOrigin) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
328 write(paste(sampleName, "\t->\t", make.names(sampleName)), stderr())
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
329 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
330 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
331 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
332
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
333 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
334 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")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
335 for (sampleName in sampleNamesOrigin) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
336 cat(paste(sampleName, "\t->\t", make.names(sampleName), "\n"))
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
337 }
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
338 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
339
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
340 sampleMetadata$sample_name <- sampleNamesMakeNames
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
341
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
342
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
343 # For each sample file, the following actions are done
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
344 for (fileIdx in seq_len(length(fileNames(xdata)))) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
345 # Check if the file is in the CDF format
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
346 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
347 # If the column isn't exist, with add one filled with NA
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
348 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
349
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
350 # Extract the polarity (a list of polarities)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
351 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx, "polarity"]
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
352 # Verify if all the scans have the same polarity
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
353 uniq_list <- unique(polarity)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
354 if (length(uniq_list) > 1) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
355 polarity <- "mixed"
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
356 } else {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
357 polarity <- as.character(uniq_list)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
358 }
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
359
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
360 # Set the polarity attribute
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
361 sampleMetadata$polarity[fileIdx] <- polarity
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
362 }
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
363 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
364
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
365 write.table(sampleMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = sampleMetadataOutput)
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
366
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
367 return(list("sampleNamesOrigin" = sampleNamesOrigin, "sampleNamesMakeNames" = sampleNamesMakeNames))
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
368 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
369
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
370
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
371 # This function will compute MD5 checksum to check the data integrity
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
372 # @author Gildas Le Corguille lecorguille@sb-roscoff.fr
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
373 getMd5sum <- function(files) {
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
374 cat("Compute md5 checksum...\n")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
375 library(tools)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
376 return(as.matrix(md5sum(files)))
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
377 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
378
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
379 # This function retrieve the raw file in the working directory
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
380 # - if zipfile: unzip the file with its directory tree
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
381 # - if singlefiles: set symlink with the good filename
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
382 # @author Gildas Le Corguille lecorguille@sb-roscoff.fr
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
383 retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") {
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
384 if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
385
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
386 # single - if the file are passed in the command arguments -> refresh singlefile
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
387 if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
388 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\|"))
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
389 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\|"))
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
390
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
391 singlefile <- NULL
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
392 for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
393 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
394 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
395 # In case, an url is used to import data within Galaxy
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
396 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName, "/")), n = 1)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
397 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
398 }
1
20f8ebc3a391 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
workflow4metabolomics
parents: 0
diff changeset
399 }
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
400 # zipfile - if the file are passed in the command arguments -> refresh zipfile
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
401 if (!is.null(args[[paste0("zipfile", prefix)]])) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
402 zipfile <- args[[paste0("zipfile", prefix)]]
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
403 }
1
20f8ebc3a391 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
workflow4metabolomics
parents: 0
diff changeset
404
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
405 # single
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
406 if (!is.null(singlefile) && (length("singlefile") > 0)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
407 files <- vector()
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
408 for (singlefile_sampleName in names(singlefile)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
409 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
410 if (!file.exists(singlefile_galaxyPath)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
411 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
412 print(error_message)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
413 stop(error_message)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
414 }
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
415
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
416 if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = TRUE))) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
417 file.copy(singlefile_galaxyPath, singlefile_sampleName)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
418 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
419 files <- c(files, singlefile_sampleName)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
420 }
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
421 }
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
422 # zipfile
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
423 if (!is.null(zipfile) && (zipfile != "")) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
424 if (!file.exists(zipfile)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
425 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
426 print(error_message)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
427 stop(error_message)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
428 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
429 suppressWarnings(unzip(zipfile, unzip = "unzip"))
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
430
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
431 # get the directory name
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
432 suppressWarnings(filesInZip <- unzip(zipfile, list = TRUE))
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
433 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
434 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
435 directory <- "."
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
436 if (length(directories) == 1) directory <- directories
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
437
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
438 cat("files_root_directory\t", directory, "\n")
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
439
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
440 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
441 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
442 info <- file.info(directory)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
443 listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
444 files <- c(directory[!info$isdir], listed)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
445 exists <- file.exists(files)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
446 files <- files[exists]
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
447 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
448 return(list(zipfile = zipfile, singlefile = singlefile, files = files))
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
449 }
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
450
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
451
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
452 # This function retrieve a xset like object
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
453 # @author Gildas Le Corguille lecorguille@sb-roscoff.fr
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
454 getxcmsSetObject <- function(xobject) {
3
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
455 # XCMS 1.x
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
456 if (class(xobject) == "xcmsSet") {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
457 return(xobject)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
458 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
459 # XCMS 3.x
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
460 if (class(xobject) == "XCMSnExp") {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
461 # Get the legacy xcmsSet object
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
462 suppressWarnings(xset <- as(xobject, "xcmsSet"))
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
463 if (!is.null(xset@phenoData$sample_group)) {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
464 sampclass(xset) <- xset@phenoData$sample_group
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
465 } else {
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
466 sampclass(xset) <- "."
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
467 }
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
468 return(xset)
6c2798bce3eb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 1
diff changeset
469 }
0
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
parents:
diff changeset
470 }