xcms_merge: lib.r annotate

annotate lib.r @ 9:e3fccadf32a8 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9

author	lecorguille
date	Thu, 07 Mar 2019 07:38:52 -0500
parents	a26679f68d4d
children	7dd38bacac3a

rev	line source
3 f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	1 #@authors ABiMS TEAM, Y. Guitton
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	3
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	4 #@author G. Le Corguille
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	5 # solve an issue with batch if arguments are logical TRUE/FALSE
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	6 parseCommandArgs <- function(...) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	7 args <- batch::parseCommandArgs(...)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	8 for (key in names(args)) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	9 if (args[key] %in% c("TRUE","FALSE"))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	10 args[key] = as.logical(args[key])
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	11 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	12 return(args)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	13 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	14
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	15 #@author G. Le Corguille
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	16 # This function will
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	17 # - load the packages
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	18 # - display the sessionInfo
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	19 loadAndDisplayPackages <- function(pkgs) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	21
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	22 sessioninfo = sessionInfo()
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	23 cat(sessioninfo$R.version$version.string,"\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	24 cat("Main packages:\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	26 cat("Other loaded packages:\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	28 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	29
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	30 #@author G. Le Corguille
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	31 # This function merge several chromBPI or chromTIC into one.
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	32 mergeChrom <- function(chrom_merged, chrom) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	33 if (is.null(chrom_merged)) return(NULL)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	34 chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	35 return(chrom_merged)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	36 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	37
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	38 #@author G. Le Corguille
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	39 # This function merge several xdata into one.
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	40 mergeXData <- function(args) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	41 chromTIC <- NULL
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	42 chromBPI <- NULL
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	43 chromTIC_adjusted <- NULL
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	44 chromBPI_adjusted <- NULL
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	45 for(image in args$images) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	46
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	47 load(image)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	48 # Handle infiles
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	49 if (!exists("singlefile")) singlefile <- NULL
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	50 if (!exists("zipfile")) zipfile <- NULL
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	51 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	52 zipfile <- rawFilePath$zipfile
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	53 singlefile <- rawFilePath$singlefile
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	54 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	55
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	56 if (exists("raw_data")) xdata <- raw_data
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	57 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	58
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	59 cat(sampleNamesList$sampleNamesOrigin,"\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	60
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	61 if (!exists("xdata_merged")) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	62 xdata_merged <- xdata
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	63 singlefile_merged <- singlefile
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	64 md5sumList_merged <- md5sumList
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	65 sampleNamesList_merged <- sampleNamesList
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	66 chromTIC_merged <- chromTIC
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	67 chromBPI_merged <- chromBPI
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	68 chromTIC_adjusted_merged <- chromTIC_adjusted
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	69 chromBPI_adjusted_merged <- chromBPI_adjusted
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	70 } else {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	71 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	72 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	73 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	74
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	75 singlefile_merged <- c(singlefile_merged,singlefile)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	76 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	77 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	78 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	79 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	80 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	81 chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	82 chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	83 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	84 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	85 rm(image)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	86 xdata <- xdata_merged; rm(xdata_merged)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	87 singlefile <- singlefile_merged; rm(singlefile_merged)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	88 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	89 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	90
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	91 if (!is.null(args$sampleMetadata)) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	92 cat("\tXSET PHENODATA SETTING...\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	93 sampleMetadataFile <- args$sampleMetadata
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	94 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	95 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	96
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	97 if (any(is.na(pData(xdata)$sample_group))) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	98 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	99 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	100 print(error_message)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	101 stop(error_message)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	102 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	103 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	104
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	105 if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	106 if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	107 if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	108 if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	109
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 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))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	111 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	112
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	113 #@author G. Le Corguille
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	114 # This function convert if it is required the Retention Time in minutes
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	115 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	116 if (convertRTMinute){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	117 #converting the retention times (seconds) into minutes
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	118 print("converting the retention times into minutes in the variableMetadata")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	119 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	120 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	121 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	122 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	123 return (variableMetadata)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	124 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	125
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	126 #@author G. Le Corguille
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	127 # This function format ions identifiers
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	128 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	129 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	130 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	131 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	132 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	133 return(variableMetadata)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	134 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	135
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	136 #@author G. Le Corguille
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	137 # This function convert the remain NA to 0 in the dataMatrix
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	138 naTOzeroDataMatrix <- function(dataMatrix, naTOzero) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	139 if (naTOzero){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	140 dataMatrix[is.na(dataMatrix)] <- 0
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	141 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	142 return (dataMatrix)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	143 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	144
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	145 #@author G. Le Corguille
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	146 # Draw the plotChromPeakDensity 3 per page in a pdf file
8 a26679f68d4d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639 lecorguille parents: 7 diff changeset	147 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit=4) {
3 f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	148 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	149
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	150 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	151
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	152 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	153 names(group_colors) <- unique(xdata$sample_group)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	154
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	155 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	156 for (i in 1:nrow(featureDefinitions(xdata))) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	157 mzmin = featureDefinitions(xdata)[i,]$mzmin
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	158 mzmax = featureDefinitions(xdata)[i,]$mzmax
8 a26679f68d4d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639 lecorguille parents: 7 diff changeset	159 plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
3 f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	160 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	161 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	162
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	163 dev.off()
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	164 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	165
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	166 #@author G. Le Corguille
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	167 # Draw the plotChromPeakDensity 3 per page in a pdf file
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	168 getPlotAdjustedRtime <- function(xdata) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	169
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	170 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	171
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	172 # Color by group
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	173 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	174 if (length(group_colors) > 1) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	175 names(group_colors) <- unique(xdata$sample_group)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	176 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	177 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	178 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	179
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	180 # Color by sample
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	181 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 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)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	183
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	184 dev.off()
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	185 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	186
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	187 #@author G. Le Corguille
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	188 # value: intensity values to be used into, maxo or intb
5 7bb43bf0b546 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty lecorguille parents: 3 diff changeset	189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
3 f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	190 dataMatrix <- featureValues(xdata, method="medret", value=intval)
5 7bb43bf0b546 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty lecorguille parents: 3 diff changeset	191 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
8 a26679f68d4d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639 lecorguille parents: 7 diff changeset	192 dataMatrix = cbind(name=groupnames(xdata), dataMatrix)
3 f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	193 variableMetadata <- featureDefinitions(xdata)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
8 a26679f68d4d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639 lecorguille parents: 7 diff changeset	195 variableMetadata = data.frame(name=groupnames(xdata), variableMetadata)
3 f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	196
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	200
7 a9d451591d7b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 5 diff changeset	201 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
a9d451591d7b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 5 diff changeset	202 variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
a9d451591d7b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 5 diff changeset	203
3 f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	204 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	205 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	206
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	207 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	208
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	209 #@author G. Le Corguille
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	210 # It allow different of field separators
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	211 getDataFrameFromFile <- function(filename, header=T) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	212 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	213 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	214 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	215 if (ncol(myDataFrame) < 2) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	216 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	217 print(error_message)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	218 stop(error_message)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	219 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	220 return(myDataFrame)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	221 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	222
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	223 #@author G. Le Corguille
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	224 # Draw the BPI and TIC graphics
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	225 # colored by sample names or class names
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	226 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	227
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	228 if (aggregationFun == "sum")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	229 type="Total Ion Chromatograms"
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	230 else
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	231 type="Base Peak Intensity Chromatograms"
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	232
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	233 adjusted="Raw"
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	234 if (hasAdjustedRtime(xdata))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	235 adjusted="Adjusted"
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	236
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	237 main <- paste(type,":",adjusted,"data")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	238
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	239 pdf(pdfname, width=16, height=10)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	240
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	241 # Color by group
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	242 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	243 if (length(group_colors) > 1) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	244 names(group_colors) <- unique(xdata$sample_group)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	245 plot(chrom, col = group_colors[chrom$sample_group], main=main)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	246 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	247 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	248
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	249 # Color by sample
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	250 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	251 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	252
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	253 dev.off()
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	254 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	255
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	256
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	257 # Get the polarities from all the samples of a condition
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	258 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	259 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	260 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	261 cat("Creating the sampleMetadata file...\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	262
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	263 #Create the sampleMetada dataframe
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	264 sampleMetadata <- xdata@phenoData@data
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	265 rownames(sampleMetadata) <- NULL
7 a9d451591d7b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 5 diff changeset	266 colnames(sampleMetadata) <- c("sample_name", "class")
3 f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	267
7 a9d451591d7b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 5 diff changeset	268 sampleNamesOrigin <- sampleMetadata$sample_name
3 f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	269 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	270
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	271 if (any(duplicated(sampleNamesMakeNames))) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	272 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	273 for (sampleName in sampleNamesOrigin) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	274 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	275 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	276 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	277 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	278
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	279 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	280 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	281 for (sampleName in sampleNamesOrigin) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	282 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	283 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	284 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	285
7 a9d451591d7b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 5 diff changeset	286 sampleMetadata$sample_name <- sampleNamesMakeNames
3 f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	287
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	288
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	289 #For each sample file, the following actions are done
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	290 for (fileIdx in 1:length(fileNames(xdata))) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	291 #Check if the file is in the CDF format
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	292 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	293
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	294 # If the column isn't exist, with add one filled with NA
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	295 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	296
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	297 #Extract the polarity (a list of polarities)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	298 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	299 #Verify if all the scans have the same polarity
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	300 uniq_list <- unique(polarity)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	301 if (length(uniq_list)>1){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	302 polarity <- "mixed"
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	303 } else {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	304 polarity <- as.character(uniq_list)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	305 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	306
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	307 #Set the polarity attribute
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	308 sampleMetadata$polarity[fileIdx] <- polarity
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	309 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	310
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	311 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	312
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	313 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	314
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	315 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	316
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	317 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	318
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	319
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	320 # This function check if xcms will found all the files
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	321 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	322 checkFilesCompatibilityWithXcms <- function(directory) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	323 cat("Checking files filenames compatibilities with xmcs...\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	324 # WHAT XCMS WILL FIND
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	325 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	326 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	327 info <- file.info(directory)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	328 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	329 files <- c(directory[!info$isdir], listed)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	330 files_abs <- file.path(getwd(), files)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	331 exists <- file.exists(files_abs)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	332 files[exists] <- files_abs[exists]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	333 files[exists] <- sub("//","/",files[exists])
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	334
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	335 # WHAT IS ON THE FILESYSTEM
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	336 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.' -not -path 'conda-env' -type f -name \"\""), intern=T)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	337 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	338
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	339 # COMPARISON
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	340 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	341 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	342 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	343 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	344 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	345 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	346
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	347
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	348 #This function list the compatible files within the directory as xcms did
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	349 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	350 getMSFiles <- function (directory) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	351 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	352 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	353 info <- file.info(directory)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	354 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	355 files <- c(directory[!info$isdir], listed)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	356 exists <- file.exists(files)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	357 files <- files[exists]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	358 return(files)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	359 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	360
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	361 # This function check if XML contains special caracters. It also checks integrity and completness.
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	362 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	363 checkXmlStructure <- function (directory) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	364 cat("Checking XML structure...\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	365
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	366 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;")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	367 capture <- system(cmd, intern=TRUE)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	368
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	369 if (length(capture)>0){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	370 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	371 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	372 write(capture, stderr())
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	373 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	374 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	375
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	376 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	377
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	378
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	379 # This function check if XML contain special characters
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	380 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	381 deleteXmlBadCharacters<- function (directory) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	382 cat("Checking Non ASCII characters in the XML...\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	383
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	384 processed <- F
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	385 l <- system( paste0("find '",directory, "' -not -name '\\.' -not -path 'conda-env' -type f -iname '.ml'"), intern=TRUE)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	386 for (i in l){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	387 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	388 capture <- suppressWarnings(system(cmd, intern=TRUE))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	389 if (length(capture)>0){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	390 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	391 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	392 c <- system(cmd, intern=TRUE)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	393 capture <- ""
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	394 processed <- T
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	395 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	396 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	397 if (processed) cat("\n\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	398 return(processed)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	399 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	400
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	401
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	402 # This function will compute MD5 checksum to check the data integrity
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	403 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	404 getMd5sum <- function (directory) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	405 cat("Compute md5 checksum...\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	406 # WHAT XCMS WILL FIND
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	407 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	408 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	409 info <- file.info(directory)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	410 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	411 files <- c(directory[!info$isdir], listed)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	412 exists <- file.exists(files)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	413 files <- files[exists]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	414
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	415 library(tools)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	416
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	417 #cat("\n\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	418
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	419 return(as.matrix(md5sum(files)))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	420 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	421
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	422
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	423 # This function get the raw file path from the arguments
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	424 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	425 getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	426 if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	427
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	428 if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	429
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	430 if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	431 singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	432 singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	433 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	434 if (exists("singlefile_galaxyPaths")){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	435 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\\|"))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	436 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\\|"))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	437
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	438 singlefile <- NULL
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	439 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	440 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	441 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	442 # In case, an url is used to import data within Galaxy
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	443 singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	444 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	445 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	446 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	447 return(list(zipfile=zipfile, singlefile=singlefile))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	448 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	449
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	450 # This function retrieve the raw file in the working directory
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	451 # - if zipfile: unzip the file with its directory tree
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	452 # - if singlefiles: set symlink with the good filename
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	453 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	454 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	455 if(!is.null(singlefile) && (length("singlefile")>0)) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	456 for (singlefile_sampleName in names(singlefile)) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	457 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	458 if(!file.exists(singlefile_galaxyPath)){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	459 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	460 print(error_message); stop(error_message)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	461 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	462
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	463 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	464 file.copy(singlefile_galaxyPath, singlefile_sampleName)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	465
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	466 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	467 directory <- "."
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	468
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	469 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	470 if(!is.null(zipfile) && (zipfile != "")) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	471 if(!file.exists(zipfile)){
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	472 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	473 print(error_message)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	474 stop(error_message)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	475 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	476
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	477 #list all file in the zip file
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	478 #zip_files <- unzip(zipfile,list=T)[,"Name"]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	479
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	480 #unzip
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	481 suppressWarnings(unzip(zipfile, unzip="unzip"))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	482
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	483 #get the directory name
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	484 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	485 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	486 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	487 directory <- "."
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	488 if (length(directories) == 1) directory <- directories
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	489
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	490 cat("files_root_directory\t",directory,"\n")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	491
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	492 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	493 return (directory)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	494 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	495
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	496
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	497 # This function retrieve a xset like object
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	498 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	499 getxcmsSetObject <- function(xobject) {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	500 # XCMS 1.x
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	501 if (class(xobject) == "xcmsSet")
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	502 return (xobject)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	503 # XCMS 3.x
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	504 if (class(xobject) == "XCMSnExp") {
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	505 # Get the legacy xcmsSet object
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	506 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	507 if (!is.null(xset@phenoData$sample_group))
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	508 sampclass(xset) <- xset@phenoData$sample_group
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	509 else
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	510 sampclass(xset) <- "."
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	511 return (xset)
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	512 }
f439ed7a8f03 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: diff changeset	513 }

Mercurial > repos > lecorguille > xcms_merge

annotate lib.r @ 9:e3fccadf32a8 draft