xcms_refine: lib.r annotate

annotate lib.r @ 1:20f8ebc3a391 draft

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e

author	workflow4metabolomics
date	Mon, 11 Sep 2023 09:19:47 +0000
parents	eb115eb8f25c
children

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

Mercurial > repos > workflow4metabolomics > xcms_refine

annotate lib.r @ 1:20f8ebc3a391 draft