xcms_export_samplemetadata: lib.r annotate

annotate lib.r @ 1:008aceb33627 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86-dirty

author	lecorguille
date	Tue, 09 Oct 2018 12:57:14 -0400
parents	e3c06320f884
children	10f7b1548200

rev	line source
0 e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	1 #@authors ABiMS TEAM, Y. Guitton
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	3
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	4 #@author G. Le Corguille
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	5 # solve an issue with batch if arguments are logical TRUE/FALSE
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	6 parseCommandArgs <- function(...) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	7 args <- batch::parseCommandArgs(...)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	8 for (key in names(args)) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	9 if (args[key] %in% c("TRUE","FALSE"))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	10 args[key] = as.logical(args[key])
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	11 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	12 return(args)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	13 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	14
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	15 #@author G. Le Corguille
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	16 # This function will
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	17 # - load the packages
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	18 # - display the sessionInfo
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	19 loadAndDisplayPackages <- function(pkgs) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	21
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	22 sessioninfo = sessionInfo()
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	23 cat(sessioninfo$R.version$version.string,"\n")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	24 cat("Main packages:\n")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	26 cat("Other loaded packages:\n")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	28 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	29
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	30 #@author G. Le Corguille
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	31 # This function merge several chromBPI or chromTIC into one.
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	32 mergeChrom <- function(chrom_merged, chrom) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	33 if (is.null(chrom_merged)) return(NULL)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	35 return(chrom_merged)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	36 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	37
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	38 #@author G. Le Corguille
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	39 # This function merge several xdata into one.
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	40 mergeXData <- function(args) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	41 chromTIC <- NULL
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	42 chromBPI <- NULL
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	43 chromTIC_adjusted <- NULL
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	44 chromBPI_adjusted <- NULL
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	45 for(image in args$images) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	46
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	47 load(image)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	48 # Handle infiles
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	49 if (!exists("singlefile")) singlefile <- NULL
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	50 if (!exists("zipfile")) zipfile <- NULL
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	51 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	52 zipfile <- rawFilePath$zipfile
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	53 singlefile <- rawFilePath$singlefile
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	54 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	55
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	56 if (exists("raw_data")) xdata <- raw_data
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	58
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	59 cat(sampleNamesList$sampleNamesOrigin,"\n")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	60
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	61 if (!exists("xdata_merged")) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	62 xdata_merged <- xdata
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	63 singlefile_merged <- singlefile
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	64 md5sumList_merged <- md5sumList
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	65 sampleNamesList_merged <- sampleNamesList
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	66 chromTIC_merged <- chromTIC
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	67 chromBPI_merged <- chromBPI
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	68 chromTIC_adjusted_merged <- chromTIC_adjusted
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	69 chromBPI_adjusted_merged <- chromBPI_adjusted
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	70 } else {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	74
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	75 singlefile_merged <- c(singlefile_merged,singlefile)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	83 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	84 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	85 rm(image)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	86 xdata <- xdata_merged; rm(xdata_merged)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	87 singlefile <- singlefile_merged; rm(singlefile_merged)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	88 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	90
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	91 if (!is.null(args$sampleMetadata)) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	92 cat("\tXSET PHENODATA SETTING...\n")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	93 sampleMetadataFile <- args$sampleMetadata
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	94 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	95 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	96
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	97 if (any(is.na(pData(xdata)$sample_group))) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	98 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	99 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	100 print(error_message)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	101 stop(error_message)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	102 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	103 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	104
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	105 if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	106 if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	107 if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	108 if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	109
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: 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))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	111 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	112
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	113 #@author G. Le Corguille
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	114 # This function convert if it is required the Retention Time in minutes
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	115 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	116 if (convertRTMinute){
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	117 #converting the retention times (seconds) into minutes
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	118 print("converting the retention times into minutes in the variableMetadata")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	119 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	120 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	121 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	122 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	123 return (variableMetadata)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	124 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	125
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	126 #@author G. Le Corguille
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	127 # This function format ions identifiers
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	128 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	129 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	130 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	131 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	132 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	133 return(variableMetadata)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	134 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	135
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	136 #@author G. Le Corguille
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	137 # This function convert the remain NA to 0 in the dataMatrix
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	138 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	139 if (naTOzero){
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	140 dataMatrix[is.na(dataMatrix)] <- 0
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	141 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	142 return (dataMatrix)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	143 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	144
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	145 #@author G. Le Corguille
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	146 # Draw the plotChromPeakDensity 3 per page in a pdf file
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	147 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	148 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	149
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	150 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	151
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	152 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	153 names(group_colors) <- unique(xdata$sample_group)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	154
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	155 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	156 for (i in 1:nrow(featureDefinitions(xdata))) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	157 mzmin = featureDefinitions(xdata)[i,]$mzmin
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	158 mzmax = featureDefinitions(xdata)[i,]$mzmax
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	159 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	160 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	161 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	162
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	163 dev.off()
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	164 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	165
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	166 #@author G. Le Corguille
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	167 # Draw the plotChromPeakDensity 3 per page in a pdf file
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	168 getPlotAdjustedRtime <- function(xdata) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	169
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	170 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	171
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	172 # Color by group
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	173 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	174 if (length(group_colors) > 1) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	175 names(group_colors) <- unique(xdata$sample_group)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	176 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	177 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	178 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	179
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	180 # Color by sample
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	181 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	182 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	183
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	184 dev.off()
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	185 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	186
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	187 #@author G. Le Corguille
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	188 # value: intensity values to be used into, maxo or intb
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	190 dataMatrix <- featureValues(xdata, method="medret", value=intval)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	191 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	192 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	193 variableMetadata <- featureDefinitions(xdata)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	195 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	196
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	200
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	201 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	202 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	203
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	204 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	205
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	206 #@author G. Le Corguille
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	207 # It allow different of field separators
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	208 getDataFrameFromFile <- function(filename, header=T) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	209 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	210 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	211 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	212 if (ncol(myDataFrame) < 2) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	213 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	214 print(error_message)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	215 stop(error_message)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	216 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	217 return(myDataFrame)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	218 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	219
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	220 #@author G. Le Corguille
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	221 # Draw the BPI and TIC graphics
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	222 # colored by sample names or class names
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	223 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	224
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	225 if (aggregationFun == "sum")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	226 type="Total Ion Chromatograms"
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	227 else
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	228 type="Base Peak Intensity Chromatograms"
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	229
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	230 adjusted="Raw"
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	231 if (hasAdjustedRtime(xdata))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	232 adjusted="Adjusted"
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	233
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	234 main <- paste(type,":",adjusted,"data")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	235
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	236 pdf(pdfname, width=16, height=10)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	237
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	238 # Color by group
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	239 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	240 if (length(group_colors) > 1) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	241 names(group_colors) <- unique(xdata$sample_group)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	242 plot(chrom, col = group_colors[chrom$sample_group], main=main)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	243 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	244 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	245
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	246 # Color by sample
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	247 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	248 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	249
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	250 dev.off()
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	251 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	252
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	253
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	254 # Get the polarities from all the samples of a condition
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	255 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	256 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	257 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	258 cat("Creating the sampleMetadata file...\n")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	259
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	260 #Create the sampleMetada dataframe
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	261 sampleMetadata <- xdata@phenoData@data
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	262 rownames(sampleMetadata) <- NULL
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	263 colnames(sampleMetadata) <- c("sample_name", "class")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	264
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	265 sampleNamesOrigin <- sampleMetadata$sample_name
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	266 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	267
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	268 if (any(duplicated(sampleNamesMakeNames))) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	269 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())
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	270 for (sampleName in sampleNamesOrigin) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	271 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	272 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	273 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	274 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	275
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	276 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	277 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")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	278 for (sampleName in sampleNamesOrigin) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	279 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	280 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	281 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	282
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	283 sampleMetadata$sample_name <- sampleNamesMakeNames
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	284
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	285
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	286 #For each sample file, the following actions are done
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	287 for (fileIdx in 1:length(fileNames(xdata))) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	288 #Check if the file is in the CDF format
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	289 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	290
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	291 # If the column isn't exist, with add one filled with NA
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	292 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	293
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	294 #Extract the polarity (a list of polarities)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	295 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	296 #Verify if all the scans have the same polarity
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	297 uniq_list <- unique(polarity)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	298 if (length(uniq_list)>1){
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	299 polarity <- "mixed"
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	300 } else {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	301 polarity <- as.character(uniq_list)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	302 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	303
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	304 #Set the polarity attribute
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	305 sampleMetadata$polarity[fileIdx] <- polarity
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	306 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	307
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	308 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	309
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	310 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	311
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	312 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	313
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	314 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	315
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	316
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	317 # This function check if xcms will found all the files
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	318 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	319 checkFilesCompatibilityWithXcms <- function(directory) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	320 cat("Checking files filenames compatibilities with xmcs...\n")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	321 # WHAT XCMS WILL FIND
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	322 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	323 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	324 info <- file.info(directory)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	325 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	326 files <- c(directory[!info$isdir], listed)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	327 files_abs <- file.path(getwd(), files)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	328 exists <- file.exists(files_abs)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	329 files[exists] <- files_abs[exists]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	330 files[exists] <- sub("//","/",files[exists])
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	331
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	332 # WHAT IS ON THE FILESYSTEM
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	333 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.' -not -path 'conda-env' -type f -name \"\""), intern=T)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	334 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	335
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	336 # COMPARISON
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	337 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	338 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	339 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	340 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	341 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	342 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	343
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	344
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	345 #This function list the compatible files within the directory as xcms did
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	346 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	347 getMSFiles <- function (directory) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	348 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	349 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	350 info <- file.info(directory)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	351 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	352 files <- c(directory[!info$isdir], listed)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	353 exists <- file.exists(files)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	354 files <- files[exists]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	355 return(files)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	356 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	357
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	358 # This function check if XML contains special caracters. It also checks integrity and completness.
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	359 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	360 checkXmlStructure <- function (directory) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	361 cat("Checking XML structure...\n")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	362
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	363 cmd <- paste0("IFS=$'\n'; for xml in $(find '",directory,"' -not -name '\\.' -not -path 'conda-env' -type f -iname '.ml'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	364 capture <- system(cmd, intern=TRUE)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	365
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	366 if (length(capture)>0){
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	367 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	368 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	369 write(capture, stderr())
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	370 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	371 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	372
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	373 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	374
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	375
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	376 # This function check if XML contain special characters
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	377 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	378 deleteXmlBadCharacters<- function (directory) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	379 cat("Checking Non ASCII characters in the XML...\n")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	380
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	381 processed <- F
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	382 l <- system( paste0("find '",directory, "' -not -name '\\.' -not -path 'conda-env' -type f -iname '.ml'"), intern=TRUE)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	383 for (i in l){
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	384 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	385 capture <- suppressWarnings(system(cmd, intern=TRUE))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	386 if (length(capture)>0){
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	387 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	388 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	389 c <- system(cmd, intern=TRUE)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	390 capture <- ""
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	391 processed <- T
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	392 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	393 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	394 if (processed) cat("\n\n")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	395 return(processed)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	396 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	397
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	398
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	399 # This function will compute MD5 checksum to check the data integrity
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	400 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	401 getMd5sum <- function (directory) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	402 cat("Compute md5 checksum...\n")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	403 # WHAT XCMS WILL FIND
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	404 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	405 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	406 info <- file.info(directory)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	407 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	408 files <- c(directory[!info$isdir], listed)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	409 exists <- file.exists(files)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	410 files <- files[exists]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	411
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	412 library(tools)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	413
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	414 #cat("\n\n")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	415
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	416 return(as.matrix(md5sum(files)))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	417 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	418
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	419
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	420 # This function get the raw file path from the arguments
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	421 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	422 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	423 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	424
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	425 if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	426
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	427 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	428 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	429 singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	430 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	431 if (exists("singlefile_galaxyPaths")){
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	432 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\\|"))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	433 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\\|"))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	434
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	435 singlefile <- NULL
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	436 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	437 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	438 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	439 # In case, an url is used to import data within Galaxy
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	440 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	441 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	442 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	443 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	444 return(list(zipfile=zipfile, singlefile=singlefile))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	445 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	446
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	447 # This function retrieve the raw file in the working directory
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	448 # - if zipfile: unzip the file with its directory tree
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	449 # - if singlefiles: set symlink with the good filename
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	450 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	451 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	452 if(!is.null(singlefile) && (length("singlefile")>0)) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	453 for (singlefile_sampleName in names(singlefile)) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	454 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	455 if(!file.exists(singlefile_galaxyPath)){
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	456 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	457 print(error_message); stop(error_message)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	458 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	459
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	460 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	461 file.copy(singlefile_galaxyPath, singlefile_sampleName)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	462
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	463 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	464 directory <- "."
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	465
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	466 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	467 if(!is.null(zipfile) && (zipfile != "")) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	468 if(!file.exists(zipfile)){
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	469 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	470 print(error_message)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	471 stop(error_message)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	472 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	473
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	474 #list all file in the zip file
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	475 #zip_files <- unzip(zipfile,list=T)[,"Name"]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	476
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	477 #unzip
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	478 suppressWarnings(unzip(zipfile, unzip="unzip"))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	479
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	480 #get the directory name
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	481 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	482 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	483 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	484 directory <- "."
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	485 if (length(directories) == 1) directory <- directories
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	486
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	487 cat("files_root_directory\t",directory,"\n")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	488
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	489 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	490 return (directory)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	491 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	492
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	493
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	494 # This function retrieve a xset like object
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	495 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	496 getxcmsSetObject <- function(xobject) {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	497 # XCMS 1.x
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	498 if (class(xobject) == "xcmsSet")
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	499 return (xobject)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	500 # XCMS 3.x
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	501 if (class(xobject) == "XCMSnExp") {
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	502 # Get the legacy xcmsSet object
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	503 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	504 if (!is.null(xset@phenoData$sample_group))
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	505 sampclass(xset) <- xset@phenoData$sample_group
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	506 else
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	507 sampclass(xset) <- "."
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	508 return (xset)
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	509 }
e3c06320f884 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86 lecorguille parents: diff changeset	510 }

Mercurial > repos > lecorguille > xcms_export_samplemetadata

annotate lib.r @ 1:008aceb33627 draft