Mercurial > repos > lecorguille > ipo

annotate lib.r @ 10:57f180a8eaae 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/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
author workflow4metabolomics
date Mon, 11 Sep 2023 22:36:51 +0000
parents 364756ea5f42
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
1 #@author G. Le Corguille
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
2 # solve an issue with batch if arguments are logical TRUE/FALSE
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
3 parseCommandArgs <- function(...) {
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
4 args <- batch::parseCommandArgs(...)
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
5 for (key in names(args)) {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
6 if (args[key] %in% c("TRUE", "FALSE"))
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
7 args[key] <- as.logical(args[key])
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
8 }
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
9 return(args)
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
10 }
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
11
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
12 #@author G. Le Corguille
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
13 # This function will
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
14 # - load the packages
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
15 # - display the sessionInfo
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
16 loadAndDisplayPackages <- function(pkgs) {
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
17 for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
18 sessioninfo <- sessionInfo()
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
19 cat(sessioninfo$R.version$version.string, "\n")
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
20 cat("Main packages:\n")
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
21 for (pkg in names(sessioninfo$otherPkgs)) {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
22 cat(paste(pkg, packageVersion(pkg)), "\t")
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
23 }
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
24 cat("\n")
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
25 cat("Other loaded packages:\n")
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
26 for (pkg in names(sessioninfo$loadedOnly)) {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
27 cat(paste(pkg, packageVersion(pkg)), "\t")
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
28 }
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
29 cat("\n")
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
30 }
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
31
3
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
32 ##
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
33 ## This function launch IPO functions to get the best parameters for xcmsSet
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
34 ## A sample among the whole dataset is used to save time
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
35 ##
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
36 ipo4xcmsSet <- function(directory, parametersOutput, args, samplebyclass = 4) {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
37 setwd(directory)
4
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62
lecorguille
parents: 3
diff changeset
38
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
39 files <- list.files(".", recursive = TRUE) # "KO/ko15.CDF" "KO/ko16.CDF" "WT/wt15.CDF" "WT/wt16.CDF"
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
40 files <- files[!files %in% c("conda_activate.log", "log.txt")]
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
41 files_classes <- basename(dirname(files)) # "KO", "KO", "WT", "WT"
6
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents: 4
diff changeset
42
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
43 mzmlfile <- files
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
44 if (samplebyclass > 0) {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
45 #random selection of N files for IPO in each class
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
46 classes <- unique(basename(dirname(files)))
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
47 mzmlfile <- NULL
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
48 for (class_i in classes){
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
49 files_class_i <- files[files_classes == class_i]
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
50 if (samplebyclass > length(files_class_i)) {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
51 mzmlfile <- c(mzmlfile, files_class_i)
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
52 } else {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
53 mzmlfile <- c(mzmlfile, sample(files_class_i, samplebyclass))
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
54 }
3
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
55 }
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
56 }
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
57 #@TODO: else, must we keep the RData to been use directly by group?
3
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
58
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
59 cat("\t\tSamples used:\n")
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
60 print(mzmlfile)
3
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
61
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
62 peakpickingParameters <- getDefaultXcmsSetStartingParams(args$method) #get default parameters of IPO
4
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62
lecorguille
parents: 3
diff changeset
63
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
64 # filter args to only get releavant parameters and complete with those that are not declared
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
65 peakpickingParametersUser <- c(args[names(args) %in% names(peakpickingParameters)], peakpickingParameters[!(names(peakpickingParameters) %in% names(args))])
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
66 peakpickingParametersUser$verbose.columns <- TRUE
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
67 resultPeakpicking <- optimizeXcmsSet(mzmlfile, peakpickingParametersUser, nSlaves = args$nSlaves, subdir = "./IPO_results") #some images generated by IPO
6
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents: 4
diff changeset
68
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
69 # export
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
70 peakpicking_best_params <- resultPeakpicking$best_settings$parameters[!(names(resultPeakpicking$best_settings$parameters) %in% c("nSlaves", "verbose.columns"))]
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
71 write.table(t(as.data.frame(peakpicking_best_params)), file = parametersOutput, sep = "\t", row.names = TRUE, col.names = FALSE, quote = FALSE) #can be read by user
6
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents: 4
diff changeset
72
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
73 return(resultPeakpicking$best_settings$xset)
6
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents: 4
diff changeset
74 }
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents: 4
diff changeset
75
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents: 4
diff changeset
76 ##
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents: 4
diff changeset
77 ## This function launch IPO functions to get the best parameters for group and retcor
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents: 4
diff changeset
78 ##
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
79 ipo4retgroup <- function(xset, directory, parametersOutput, args, samplebyclass = 4) {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
80 setwd(directory)
3
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
81
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
82 files <- list.files(".", recursive = TRUE) # "KO/ko15.CDF" "KO/ko16.CDF" "WT/wt15.CDF" "WT/wt16.CDF"
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
83 files <- files[!files %in% c("conda_activate.log", "log.txt")]
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
84 files_classes <- basename(dirname(files)) # "KO", "KO", "WT", "WT"
6
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents: 4
diff changeset
85
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
86 retcorGroupParameters <- getDefaultRetGroupStartingParams(args$retcorMethod) #get default parameters of IPO
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
87 print(retcorGroupParameters)
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
88 # filter args to only get releavant parameters and complete with those that are not declared
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
89 retcorGroupParametersUser <- c(args[names(args) %in% names(retcorGroupParameters)], retcorGroupParameters[!(names(retcorGroupParameters) %in% names(args))])
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
90 print("retcorGroupParametersUser")
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
91 print(retcorGroupParametersUser)
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
92 resultRetcorGroup <- optimizeRetGroup(xset, retcorGroupParametersUser, nSlaves = args$nSlaves, subdir = "../IPO_results") #some images generated by IPO
6
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents: 4
diff changeset
93
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
94 # export
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
95 resultRetcorGroup_best_params <- resultRetcorGroup$best_settings
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
96 write.table(t(as.data.frame(resultRetcorGroup_best_params)), file = parametersOutput, sep = "\t", row.names = TRUE, col.names = FALSE, quote = FALSE) #can be read by user
3
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
97 }
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
98
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
99
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
100
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
101 # This function check if XML contains special caracters. It also checks integrity and completness.
3
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
102 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
103 checkXmlStructure <- function(directory) {
3
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
104 cat("Checking XML structure...\n")
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
105
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
106 cmd <- paste0("IFS=$'\n'; for xml in $(find '", directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
107 capture <- system(cmd, intern = TRUE)
3
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
108
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
109 if (length(capture) > 0) {
3
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
110 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
111 write(capture, stderr())
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
112 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
113 }
6
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
lecorguille
parents: 4
diff changeset
114
3
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty
lecorguille
parents:
diff changeset
115 }
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
116
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
117
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
118 # This function get the raw file path from the arguments
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
119 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
120 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix = "") {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
121 if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
122
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
123 if (!is.null(args[[paste0("zipfile", prefix)]])) zipfile <- args[[paste0("zipfile", prefix)]]
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
124
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
125 if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
126 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath", prefix)]]
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
127 singlefile_sampleNames <- args[[paste0("singlefile_sampleName", prefix)]]
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
128 }
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
129 if (exists("singlefile_galaxyPaths")) {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
130 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths, "\\|"))
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
131 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames, "\\|"))
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
132
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
133 singlefile <- NULL
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
134 for (singlefile_galaxyPath_i in seq_along(length(singlefile_galaxyPaths))) {
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
135 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
136 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
137 # In case, an url is used to import data within Galaxy
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
138 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName, "/")), n = 1)
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
139 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
140 }
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
141 }
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
142 return(list(zipfile = zipfile, singlefile = singlefile))
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
143 }
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
144
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
145 # This function retrieve the raw file in the working directory
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
146 # - if zipfile: unzip the file with its directory tree
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
147 # - if singlefiles: set symlink with the good filename
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
148 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
149 retrieveRawfileInWD <- function(singlefile, zipfile) {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
150 if (!is.null(singlefile) && (length("singlefile") > 0)) {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
151 for (singlefile_sampleName in names(singlefile)) {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
152 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
153 if (!file.exists(singlefile_galaxyPath)) {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
154 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
155 print(error_message)
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
156 stop(error_message)
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
157 }
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
158
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
159 if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = TRUE)))
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
160 file.copy(singlefile_galaxyPath, singlefile_sampleName)
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
161
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
162 }
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
163 directory <- "."
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
164
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
165 }
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
166 if (!is.null(zipfile) && (zipfile != "")) {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
167 if (!file.exists(zipfile)) {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
168 error_message <- paste(
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
169 "Cannot access the Zip file:",
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
170 zipfile,
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
171 ". Please, contact your administrator ... if you have one!"
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
172 )
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
173 print(error_message)
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
174 stop(error_message)
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
175 }
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
176
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
177 #unzip
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
178 suppressWarnings(unzip(zipfile, unzip = "unzip"))
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
179
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
180 #get the directory name
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
181 suppressWarnings(filesInZip <- unzip(zipfile, list = TRUE))
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
182 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
183 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
184 directory <- "."
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
185 if (length(directories) == 1) directory <- directories
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
186
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
187 cat("files_root_directory\t", directory, "\n")
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
188
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
189 }
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
190 return(directory)
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
191 }
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
192
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
193
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
194 # This function retrieve a xset like object
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
195 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
196 getxcmsSetObject <- function(xobject) {
10
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
197 # XCMS 1.x
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
198 if (class(xobject) == "xcmsSet")
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
199 return(xobject)
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
200 # XCMS 3.x
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
201 if (class(xobject) == "XCMSnExp") {
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
202 # Get the legacy xcmsSet object
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
203 suppressWarnings(xset <- as(xobject, "xcmsSet"))
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
204 if (!is.null(xset@phenoData$sample_group))
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
205 sampclass(xset) <- xset@phenoData$sample_group
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
206 else
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
207 sampclass(xset) <- "."
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
208 return(xset)
57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
workflow4metabolomics
parents: 9
diff changeset
209 }
9
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97"
workflow4metabolomics
parents: 6
diff changeset
210 }