xcms_fillpeaks: lib.r annotate

annotate lib.r @ 24:999f9db0ca2c draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"

author	workflow4metabolomics
date	Wed, 12 Feb 2020 08:28:33 -0500
parents	6824468351ca
children	26d77e9ceb49

rev	line source
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	1 #@authors ABiMS TEAM, Y. Guitton
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	3
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	4 #@author G. Le Corguille
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	5 # solve an issue with batch if arguments are logical TRUE/FALSE
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	6 parseCommandArgs <- function(...) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	7 args <- batch::parseCommandArgs(...)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	8 for (key in names(args)) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	9 if (args[key] %in% c("TRUE","FALSE"))
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	10 args[key] = as.logical(args[key])
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	11 }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	12 return(args)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	13 }
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	14
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	15 #@author G. Le Corguille
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	16 # This function will
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	17 # - load the packages
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	18 # - display the sessionInfo
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	19 loadAndDisplayPackages <- function(pkgs) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	21
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	22 sessioninfo = sessionInfo()
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	23 cat(sessioninfo$R.version$version.string,"\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	24 cat("Main packages:\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	26 cat("Other loaded packages:\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	28 }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	29
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	30 #@author G. Le Corguille
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	31 # This function merge several chromBPI or chromTIC into one.
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	32 mergeChrom <- function(chrom_merged, chrom) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	33 if (is.null(chrom_merged)) return(NULL)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	35 return(chrom_merged)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	36 }
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	37
9 ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	38 #@author G. Le Corguille
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	39 # This function merge several xdata into one.
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	40 mergeXData <- function(args) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	41 chromTIC <- NULL
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	42 chromBPI <- NULL
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	43 chromTIC_adjusted <- NULL
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	44 chromBPI_adjusted <- NULL
24 999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	45 md5sumList <- NULL
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	46 for(image in args$images) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	47
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	48 load(image)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	49 # Handle infiles
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	50 if (!exists("singlefile")) singlefile <- NULL
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	51 if (!exists("zipfile")) zipfile <- NULL
24 999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	52 rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	53 zipfile <- rawFilePath$zipfile
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	54 singlefile <- rawFilePath$singlefile
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	55
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	56 if (exists("raw_data")) xdata <- raw_data
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	58
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	59 cat(sampleNamesList$sampleNamesOrigin,"\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	60
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	61 if (!exists("xdata_merged")) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	62 xdata_merged <- xdata
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	63 singlefile_merged <- singlefile
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	64 md5sumList_merged <- md5sumList
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	65 sampleNamesList_merged <- sampleNamesList
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	66 chromTIC_merged <- chromTIC
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	67 chromBPI_merged <- chromBPI
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	68 chromTIC_adjusted_merged <- chromTIC_adjusted
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	69 chromBPI_adjusted_merged <- chromBPI_adjusted
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	70 } else {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
20 c0e7d2fae9ee planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4632d03b53c344757d71dd3310d37069fb498b26 lecorguille parents: 18 diff changeset	72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata)
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	74
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	75 singlefile_merged <- c(singlefile_merged,singlefile)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	83 }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	84 }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	85 rm(image)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	86 xdata <- xdata_merged; rm(xdata_merged)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	87 singlefile <- singlefile_merged; rm(singlefile_merged)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	88 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	90
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	91 if (!is.null(args$sampleMetadata)) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	92 cat("\tXSET PHENODATA SETTING...\n")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	93 sampleMetadataFile <- args$sampleMetadata
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	94 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	95 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	96
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	97 if (any(is.na(pData(xdata)$sample_group))) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	98 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	99 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	100 print(error_message)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	101 stop(error_message)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	102 }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	103 }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	104
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	105 if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	106 if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	107 if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	108 if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	109
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	110 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted))
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	111 }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	112
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	113 #@author G. Le Corguille
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	114 # This function convert if it is required the Retention Time in minutes
9 ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	115 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	116 if (convertRTMinute){
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	117 #converting the retention times (seconds) into minutes
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	118 print("converting the retention times into minutes in the variableMetadata")
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	119 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	120 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	121 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
9 ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	122 }
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	123 return (variableMetadata)
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	124 }
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	125
9 ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	126 #@author G. Le Corguille
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	127 # This function format ions identifiers
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	128 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	129 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	130 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	131 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	132 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	133 return(variableMetadata)
9 ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	134 }
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	135
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	136 #@author G. Le Corguille
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	137 # This function convert the remain NA to 0 in the dataMatrix
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	138 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	139 if (naTOzero){
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	140 dataMatrix[is.na(dataMatrix)] <- 0
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	141 }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	142 return (dataMatrix)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	143 }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	144
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	145 #@author G. Le Corguille
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	146 # Draw the plotChromPeakDensity 3 per page in a pdf file
18 27fbe73c4279 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639 lecorguille parents: 17 diff changeset	147 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit=4) {
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	148 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	149
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	150 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	151
24 999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	152 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	153 names(group_colors) <- unique(xdata$sample_group)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	154
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	155 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	156 for (i in 1:nrow(featureDefinitions(xdata))) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	157 mzmin = featureDefinitions(xdata)[i,]$mzmin
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	158 mzmax = featureDefinitions(xdata)[i,]$mzmax
18 27fbe73c4279 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639 lecorguille parents: 17 diff changeset	159 plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	160 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	161 }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	162
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	163 dev.off()
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	164 }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	165
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	166 #@author G. Le Corguille
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	167 # Draw the plotChromPeakDensity 3 per page in a pdf file
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	168 getPlotAdjustedRtime <- function(xdata) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	169
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	170 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	171
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	172 # Color by group
24 999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	173 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	174 if (length(group_colors) > 1) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	175 names(group_colors) <- unique(xdata$sample_group)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	176 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	177 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	178 }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	179
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	180 # Color by sample
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	181 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	182 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	183
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	184 dev.off()
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	185 }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	186
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	187 #@author G. Le Corguille
9 ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	188 # value: intensity values to be used into, maxo or intb
15 1b60d8eb704a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty lecorguille parents: 13 diff changeset	189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	190 dataMatrix <- featureValues(xdata, method="medret", value=intval)
15 1b60d8eb704a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty lecorguille parents: 13 diff changeset	191 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
18 27fbe73c4279 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639 lecorguille parents: 17 diff changeset	192 dataMatrix = cbind(name=groupnames(xdata), dataMatrix)
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	193 variableMetadata <- featureDefinitions(xdata)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
18 27fbe73c4279 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639 lecorguille parents: 17 diff changeset	195 variableMetadata = data.frame(name=groupnames(xdata), variableMetadata)
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	196
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
9 ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	200
17 b6b62413936f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 15 diff changeset	201 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
b6b62413936f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 15 diff changeset	202 variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
b6b62413936f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 15 diff changeset	203
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	204 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	205 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	206
9 ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	207 }
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	208
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	209 #@author G. Le Corguille
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	210 # It allow different of field separators
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	211 getDataFrameFromFile <- function(filename, header=T) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	212 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	213 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	214 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	215 if (ncol(myDataFrame) < 2) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	216 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	217 print(error_message)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	218 stop(error_message)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	219 }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	220 return(myDataFrame)
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	221 }
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	222
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	223 #@author G. Le Corguille
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	224 # Draw the BPI and TIC graphics
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	225 # colored by sample names or class names
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	226 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	227
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	228 if (aggregationFun == "sum")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	229 type="Total Ion Chromatograms"
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	230 else
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	231 type="Base Peak Intensity Chromatograms"
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	232
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	233 adjusted="Raw"
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	234 if (hasAdjustedRtime(xdata))
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	235 adjusted="Adjusted"
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	236
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	237 main <- paste(type,":",adjusted,"data")
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	238
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	239 pdf(pdfname, width=16, height=10)
9 ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	240
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	241 # Color by group
24 999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	242 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	243 if (length(group_colors) > 1) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	244 names(group_colors) <- unique(xdata$sample_group)
24 999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	245 plot(chrom, col = group_colors[as.factor(chrom$sample_group)], main=main, peakType = "none")
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	246 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	247 }
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	248
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	249 # Color by sample
24 999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	250 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main, peakType = "none")
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	251 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	252
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	253 dev.off()
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	254 }
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	255
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	256
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	257 # Get the polarities from all the samples of a condition
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	258 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	259 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	260 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	261 cat("Creating the sampleMetadata file...\n")
9 ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 4 diff changeset	262
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	263 #Create the sampleMetada dataframe
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	264 sampleMetadata <- xdata@phenoData@data
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	265 rownames(sampleMetadata) <- NULL
17 b6b62413936f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 15 diff changeset	266 colnames(sampleMetadata) <- c("sample_name", "class")
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	267
17 b6b62413936f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 15 diff changeset	268 sampleNamesOrigin <- sampleMetadata$sample_name
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	269 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	270
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	271 if (any(duplicated(sampleNamesMakeNames))) {
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	272 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())
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	273 for (sampleName in sampleNamesOrigin) {
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	274 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	275 }
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	276 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	277 }
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	278
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	279 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	280 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")
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	281 for (sampleName in sampleNamesOrigin) {
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	282 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	283 }
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	284 }
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	285
17 b6b62413936f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 15 diff changeset	286 sampleMetadata$sample_name <- sampleNamesMakeNames
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	287
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	288
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	289 #For each sample file, the following actions are done
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	290 for (fileIdx in 1:length(fileNames(xdata))) {
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	291 #Check if the file is in the CDF format
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	292 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	293
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	294 # If the column isn't exist, with add one filled with NA
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	295 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	296
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	297 #Extract the polarity (a list of polarities)
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	298 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	299 #Verify if all the scans have the same polarity
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	300 uniq_list <- unique(polarity)
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	301 if (length(uniq_list)>1){
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	302 polarity <- "mixed"
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	303 } else {
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	304 polarity <- as.character(uniq_list)
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	305 }
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	306
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	307 #Set the polarity attribute
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	308 sampleMetadata$polarity[fileIdx] <- polarity
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	309 }
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	310
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	311 }
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	312
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	313 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	314
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	315 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	316
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	317 }
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	318
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	319
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	320 # This function will compute MD5 checksum to check the data integrity
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	321 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
24 999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	322 getMd5sum <- function (files) {
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	323 cat("Compute md5 checksum...\n")
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	324 library(tools)
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	325 return(as.matrix(md5sum(files)))
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	326 }
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	327
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	328 # This function retrieve the raw file in the working directory
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	329 # - if zipfile: unzip the file with its directory tree
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	330 # - if singlefiles: set symlink with the good filename
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	331 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
24 999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	332 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile, args, prefix="") {
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	333
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	334 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	335
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	336 # single - if the file are passed in the command arguments -> refresh singlefile
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	337 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	338 singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath",prefix)]],"\\\|"))
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	339 singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName",prefix)]],"\\\|"))
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	340
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	341 singlefile <- NULL
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	342 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	343 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	344 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	345 # In case, an url is used to import data within Galaxy
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	346 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	347 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	348 }
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	349 }
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	350 # zipfile - if the file are passed in the command arguments -> refresh zipfile
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	351 if (!is.null(args[[paste0("zipfile",prefix)]]))
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	352 zipfile <- args[[paste0("zipfile",prefix)]]
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	353
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	354 # single
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	355 if(!is.null(singlefile) && (length("singlefile")>0)) {
24 999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	356 files <- vector()
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	357 for (singlefile_sampleName in names(singlefile)) {
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	358 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	359 if(!file.exists(singlefile_galaxyPath)){
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	360 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	361 print(error_message); stop(error_message)
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	362 }
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	363
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	364 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	365 file.copy(singlefile_galaxyPath, singlefile_sampleName)
24 999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	366 files <- c(files, singlefile_sampleName)
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	367 }
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	368 }
24 999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	369 # zipfile
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	370 if(!is.null(zipfile) && (zipfile != "")) {
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	371 if(!file.exists(zipfile)){
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	372 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	373 print(error_message)
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	374 stop(error_message)
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	375 }
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	376 suppressWarnings(unzip(zipfile, unzip="unzip"))
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	377
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	378 #get the directory name
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	379 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	380 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	381 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	382 directory <- "."
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	383 if (length(directories) == 1) directory <- directories
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	384
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	385 cat("files_root_directory\t",directory,"\n")
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	386
24 999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	387 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	388 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	389 info <- file.info(directory)
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	390 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	391 files <- c(directory[!info$isdir], listed)
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	392 exists <- file.exists(files)
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	393 files <- files[exists]
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	394
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	395 }
24 999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	396 return(list(zipfile=zipfile, singlefile=singlefile, files=files))
999f9db0ca2c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 22 diff changeset	397
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: diff changeset	398 }
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	399
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	400
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	401 # This function retrieve a xset like object
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	402 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	403 getxcmsSetObject <- function(xobject) {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	404 # XCMS 1.x
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	405 if (class(xobject) == "xcmsSet")
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	406 return (xobject)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	407 # XCMS 3.x
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	408 if (class(xobject) == "XCMSnExp") {
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	409 # Get the legacy xcmsSet object
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	410 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	411 if (!is.null(xset@phenoData$sample_group))
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	412 sampclass(xset) <- xset@phenoData$sample_group
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	413 else
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	414 sampclass(xset) <- "."
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	415 return (xset)
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	416 }
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 11 diff changeset	417 }

Mercurial > repos > lecorguille > xcms_fillpeaks

annotate lib.r @ 24:999f9db0ca2c draft