msnbase_readmsdata: lib.r annotate

annotate lib.r @ 0:24f7d4e5c186 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty

author	lecorguille
date	Tue, 03 Apr 2018 11:50:50 -0400
parents
children	fa17ee3bc9ce

rev	line source
0 24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	1 #@authors ABiMS TEAM, Y. Guitton
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	3
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	4 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	5 # solve an issue with batch if arguments are logical TRUE/FALSE
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	6 parseCommandArgs <- function(...) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	7 args <- batch::parseCommandArgs(...)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	8 for (key in names(args)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	9 if (args[key] %in% c("TRUE","FALSE"))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	10 args[key] = as.logical(args[key])
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	11 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	12 return(args)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	13 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	14
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	15 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	16 # This function will
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	17 # - load the packages
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	18 # - display the sessionInfo
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	19 loadAndDisplayPackages <- function(pkgs) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	21
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	22 sessioninfo = sessionInfo()
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	23 cat(sessioninfo$R.version$version.string,"\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	24 cat("Main packages:\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	26 cat("Other loaded packages:\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	28 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	29
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	30 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	31 # This function merge several xdata into one.
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	32 mergeXData <- function(args) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	33 for(image in args$images) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	34 load(image)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	35 # Handle infiles
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	36 if (!exists("singlefile")) singlefile <- NULL
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	37 if (!exists("zipfile")) zipfile <- NULL
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	38 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	39 zipfile <- rawFilePath$zipfile
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	40 singlefile <- rawFilePath$singlefile
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	41 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	42 if (exists("raw_data")) xdata <- raw_data
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	43 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	44 cat(sampleNamesList$sampleNamesOrigin,"\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	45 if (!exists("xdata_merged")) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	46 xdata_merged <- xdata
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	47 singlefile_merged <- singlefile
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	48 md5sumList_merged <- md5sumList
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	49 sampleNamesList_merged <- sampleNamesList
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	50 } else {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	51 if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	52 else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	53 else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	54 singlefile_merged <- c(singlefile_merged,singlefile)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	55 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	56 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	57 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	58 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	59 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	60 rm(image)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	61 xdata <- xdata_merged; rm(xdata_merged)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	62 singlefile <- singlefile_merged; rm(singlefile_merged)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	63 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	64 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	65
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	66 if (!is.null(args$sampleMetadata)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	67 cat("\tXSET PHENODATA SETTING...\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	68 sampleMetadataFile <- args$sampleMetadata
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	69 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	70 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	71
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	72 if (any(is.na(pData(xdata)$sample_group))) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	73 sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	74 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	75 print(error_message)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	76 stop(error_message)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	77 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	78 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	79 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	80 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	81
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	82 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	83 # This function convert if it is required the Retention Time in minutes
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	84 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	85 if (convertRTMinute){
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	86 #converting the retention times (seconds) into minutes
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	87 print("converting the retention times into minutes in the variableMetadata")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	88 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	89 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	90 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	91 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	92 return (variableMetadata)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	93 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	94
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	95 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	96 # This function format ions identifiers
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	97 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	98 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	99 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	100 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	101 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	102 return(variableMetadata)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	103 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	104
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	105 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	106 # Draw the plotChromPeakDensity 3 per page in a pdf file
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	107 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	108 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	109
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	110 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	111
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	112 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	113 names(group_colors) <- unique(xdata$sample_group)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	114
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	115 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	116 for (i in 1:nrow(featureDefinitions(xdata))) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	117 mzmin = featureDefinitions(xdata)[i,]$mzmin
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	118 mzmax = featureDefinitions(xdata)[i,]$mzmax
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	119 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	120 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	121 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	122
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	123 dev.off()
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	124 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	125
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	126 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	127 # Draw the plotChromPeakDensity 3 per page in a pdf file
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	128 getPlotAdjustedRtime <- function(xdata) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	129
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	130 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	131
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	132 # Color by group
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	133 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	134 if (length(group_colors) > 1) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	135 names(group_colors) <- unique(xdata$sample_group)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	136 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	137 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	138 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	139
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	140 # Color by sample
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	141 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	142 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	143
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	144 dev.off()
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	145 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	146
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	147 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	148 # value: intensity values to be used into, maxo or intb
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	149 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	150 dataMatrix <- featureValues(xdata, method="medret", value=intval)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	151 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	152 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	153 variableMetadata <- featureDefinitions(xdata)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	154 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	155 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	156
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	157 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	158 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	159
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	160 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	161 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	162
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	163 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	164
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	165 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	166 # It allow different of field separators
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	167 getDataFrameFromFile <- function(filename, header=T) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	168 myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	169 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	170 if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	171 if (ncol(myDataFrame) < 2) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	172 error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation"
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	173 print(error_message)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	174 stop(error_message)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	175 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	176 return(myDataFrame)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	177 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	178
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	179 getPlotChromatogram <- function(xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	180
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	181 chrom <- chromatogram(xdata, aggregationFun = aggregationFun)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	182 if (aggregationFun == "sum")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	183 type="Total Ion Chromatograms"
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	184 else
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	185 type="Base Peak Intensity Chromatograms"
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	186
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	187 adjusted="Raw"
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	188 if (hasAdjustedRtime(xdata))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	189 adjusted="Adjusted"
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	190
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	191 main <- paste(type,":",adjusted,"data")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	192
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	193 pdf(pdfname, width=16, height=10)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	194
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	195 # Color by group
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	196 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	197 if (length(group_colors) > 1) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	198 names(group_colors) <- unique(xdata$sample_group)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	199 plot(chrom, col = group_colors[chrom$sample_group], main=main)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	200 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	201 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	202
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	203 # Color by sample
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	204 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	205 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	206
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	207 dev.off()
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	208 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	209
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	210 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	211 getPlotTICs <- function(xdata, pdfname="TICs.pdf") {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	212 getPlotChromatogram(xdata, pdfname, aggregationFun = "sum")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	213 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	214
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	215 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	216 getPlotBPIs <- function(xdata, pdfname="BPIs.pdf") {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	217 getPlotChromatogram(xdata, pdfname, aggregationFun = "max")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	218 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	219
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	220
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	221 # Get the polarities from all the samples of a condition
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	222 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	223 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	224 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	225 cat("Creating the sampleMetadata file...\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	226
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	227 #Create the sampleMetada dataframe
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	228 sampleMetadata <- xdata@phenoData@data
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	229 rownames(sampleMetadata) <- NULL
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	230 colnames(sampleMetadata) <- c("sampleMetadata", "class")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	231
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	232 sampleNamesOrigin <- sampleMetadata$sampleMetadata
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	233 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	234
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	235 if (any(duplicated(sampleNamesMakeNames))) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	236 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())
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	237 for (sampleName in sampleNamesOrigin) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	238 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	239 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	240 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	241 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	242
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	243 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	244 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")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	245 for (sampleName in sampleNamesOrigin) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	246 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	247 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	248 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	249
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	250 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	251
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	252
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	253 #For each sample file, the following actions are done
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	254 for (fileIdx in 1:length(fileNames(xdata))) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	255 #Check if the file is in the CDF format
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	256 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	257
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	258 # If the column isn't exist, with add one filled with NA
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	259 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	260
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	261 #Extract the polarity (a list of polarities)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	262 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	263 #Verify if all the scans have the same polarity
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	264 uniq_list <- unique(polarity)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	265 if (length(uniq_list)>1){
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	266 polarity <- "mixed"
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	267 } else {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	268 polarity <- as.character(uniq_list)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	269 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	270
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	271 #Set the polarity attribute
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	272 sampleMetadata$polarity[fileIdx] <- polarity
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	273 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	274
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	275 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	276
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	277 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	278
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	279 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	280
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	281 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	282
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	283
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	284 # This function check if xcms will found all the files
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	285 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	286 checkFilesCompatibilityWithXcms <- function(directory) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	287 cat("Checking files filenames compatibilities with xmcs...\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	288 # WHAT XCMS WILL FIND
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	289 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	290 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	291 info <- file.info(directory)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	292 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	293 files <- c(directory[!info$isdir], listed)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	294 files_abs <- file.path(getwd(), files)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	295 exists <- file.exists(files_abs)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	296 files[exists] <- files_abs[exists]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	297 files[exists] <- sub("//","/",files[exists])
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	298
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	299 # WHAT IS ON THE FILESYSTEM
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	300 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.' -not -path 'conda-env' -type f -name \"\""), intern=T)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	301 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	302
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	303 # COMPARISON
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	304 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	305 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	306 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	307 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	308 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	309 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	310
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	311
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	312 #This function list the compatible files within the directory as xcms did
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	313 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	314 getMSFiles <- function (directory) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	315 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	316 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	317 info <- file.info(directory)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	318 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	319 files <- c(directory[!info$isdir], listed)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	320 exists <- file.exists(files)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	321 files <- files[exists]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	322 return(files)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	323 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	324
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	325 # This function check if XML contains special caracters. It also checks integrity and completness.
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	326 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	327 checkXmlStructure <- function (directory) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	328 cat("Checking XML structure...\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	329
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	330 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;")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	331 capture <- system(cmd, intern=TRUE)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	332
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	333 if (length(capture)>0){
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	334 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	335 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	336 write(capture, stderr())
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	337 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	338 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	339
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	340 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	341
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	342
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	343 # This function check if XML contain special characters
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	344 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	345 deleteXmlBadCharacters<- function (directory) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	346 cat("Checking Non ASCII characters in the XML...\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	347
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	348 processed <- F
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	349 l <- system( paste0("find '",directory, "' -not -name '\\.' -not -path 'conda-env' -type f -iname '.ml'"), intern=TRUE)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	350 for (i in l){
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	351 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	352 capture <- suppressWarnings(system(cmd, intern=TRUE))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	353 if (length(capture)>0){
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	354 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	355 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	356 c <- system(cmd, intern=TRUE)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	357 capture <- ""
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	358 processed <- T
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	359 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	360 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	361 if (processed) cat("\n\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	362 return(processed)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	363 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	364
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	365
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	366 # This function will compute MD5 checksum to check the data integrity
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	367 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	368 getMd5sum <- function (directory) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	369 cat("Compute md5 checksum...\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	370 # WHAT XCMS WILL FIND
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	371 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	372 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	373 info <- file.info(directory)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	374 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	375 files <- c(directory[!info$isdir], listed)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	376 exists <- file.exists(files)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	377 files <- files[exists]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	378
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	379 library(tools)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	380
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	381 #cat("\n\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	382
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	383 return(as.matrix(md5sum(files)))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	384 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	385
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	386
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	387 # This function get the raw file path from the arguments
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	388 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	389 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	390 if (!is.null(args$zipfile)) zipfile <- args$zipfile
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	391 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	392 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	393
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	394 if (!is.null(args$singlefile_galaxyPath)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	395 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	396 singlefile_sampleNames <- args$singlefile_sampleName
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	397 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	398 if (!is.null(args$singlefile_galaxyPathPositive)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	399 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	400 singlefile_sampleNames <- args$singlefile_sampleNamePositive
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	401 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	402 if (!is.null(args$singlefile_galaxyPathNegative)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	403 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	404 singlefile_sampleNames <- args$singlefile_sampleNameNegative
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	405 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	406 if (exists("singlefile_galaxyPaths")){
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	407 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\\|"))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	408 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\\|"))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	409
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	410 singlefile <- NULL
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	411 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	412 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	413 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	414 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	415 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	416 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	417 return(list(zipfile=zipfile, singlefile=singlefile))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	418 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	419
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	420
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	421 # This function retrieve the raw file in the working directory
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	422 # - if zipfile: unzip the file with its directory tree
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	423 # - if singlefiles: set symlink with the good filename
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	424 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	425 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	426 if(!is.null(singlefile) && (length("singlefile")>0)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	427 for (singlefile_sampleName in names(singlefile)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	428 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	429 if(!file.exists(singlefile_galaxyPath)){
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	430 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	431 print(error_message); stop(error_message)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	432 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	433
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	434 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	435 file.copy(singlefile_galaxyPath, singlefile_sampleName)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	436
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	437 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	438 directory <- "."
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	439
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	440 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	441 if(!is.null(zipfile) && (zipfile != "")) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	442 if(!file.exists(zipfile)){
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	443 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	444 print(error_message)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	445 stop(error_message)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	446 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	447
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	448 #list all file in the zip file
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	449 #zip_files <- unzip(zipfile,list=T)[,"Name"]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	450
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	451 #unzip
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	452 suppressWarnings(unzip(zipfile, unzip="unzip"))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	453
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	454 #get the directory name
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	455 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	456 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	457 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	458 directory <- "."
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	459 if (length(directories) == 1) directory <- directories
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	460
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	461 cat("files_root_directory\t",directory,"\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	462
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	463 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	464 return (directory)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	465 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	466
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	467
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	468 # This function retrieve a xset like object
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	469 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	470 getxcmsSetObject <- function(xobject) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	471 # XCMS 1.x
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	472 if (class(xobject) == "xcmsSet")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	473 return (xobject)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	474 # XCMS 3.x
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	475 if (class(xobject) == "XCMSnExp") {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	476 # Get the legacy xcmsSet object
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	477 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	478 sampclass(xset) <- xset@phenoData$sample_group
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	479 return (xset)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	480 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	481 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	482
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	483
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	484 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	485 # https://github.com/sneumann/xcms/issues/250
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	486 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	487 mzfmt <- paste("%.", mzdec, "f", sep = "")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	488 rtfmt <- paste("%.", rtdec, "f", sep = "")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	489
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	490 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	491 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	492
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	493 if (any(dup <- duplicated(gnames)))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	494 for (dupname in unique(gnames[dup])) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	495 dupidx <- which(gnames == dupname)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	496 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	497 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	498
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	499 return (gnames)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	500 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	501
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	502 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	503 # https://github.com/sneumann/xcms/issues/247
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	504 .concatenate_XCMSnExp <- function(...) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	505 x <- list(...)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	506 if (length(x) == 0)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	507 return(NULL)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	508 if (length(x) == 1)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	509 return(x[[1]])
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	510 ## Check that all are XCMSnExp objects.
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	511 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	512 stop("All passed objects should be 'XCMSnExp' objects")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	513 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	514 ## If any of the XCMSnExp has alignment results or detected features drop
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	515 ## them!
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	516 x <- lapply(x, function(z) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	517 if (hasAdjustedRtime(z)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	518 z <- dropAdjustedRtime(z)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	519 warning("Adjusted retention times found, had to drop them.")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	520 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	521 if (hasFeatures(z)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	522 z <- dropFeatureDefinitions(z)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	523 warning("Feature definitions found, had to drop them.")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	524 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	525 z
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	526 })
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	527 ## Combine peaks
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	528 fls <- lapply(x, fileNames)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	529 startidx <- cumsum(lengths(fls))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	530 pks <- lapply(x, chromPeaks)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	531 procH <- lapply(x, processHistory)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	532 for (i in 2:length(fls)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	533 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	534 procH[[i]] <- lapply(procH[[i]], function(z) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	535 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	536 z
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	537 })
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	538 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	539 pks <- do.call(rbind, pks)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	540 new_x@.processHistory <- unlist(procH)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	541 chromPeaks(new_x) <- pks
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	542 if (validObject(new_x))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	543 new_x
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	544 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	545
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	546 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	547 # https://github.com/sneumann/xcms/issues/247
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	548 .concatenate_OnDiskMSnExp <- function(...) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	549 x <- list(...)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	550 if (length(x) == 0)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	551 return(NULL)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	552 if (length(x) == 1)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	553 return(x[[1]])
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	554 ## Check that all are XCMSnExp objects.
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	555 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	556 stop("All passed objects should be 'OnDiskMSnExp' objects")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	557 ## Check processingQueue
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	558 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	559 new_procQ <- procQ[[1]]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	560 is_ok <- unlist(lapply(procQ, function(z)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	561 !is.character(all.equal(new_procQ, z))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	562 ))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	563 if (any(!is_ok)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	564 warning("Processing queues from the submitted objects differ! ",
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	565 "Dropping the processing queue.")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	566 new_procQ <- list()
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	567 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	568 ## processingData
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	569 fls <- lapply(x, function(z) z@processingData@files)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	570 startidx <- cumsum(lengths(fls))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	571 ## featureData
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	572 featd <- lapply(x, fData)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	573 ## Have to update the file index and the spectrum names.
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	574 for (i in 2:length(featd)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	575 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	576 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	577 fileIds = featd[[i]]$fileIdx,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	578 spectrumIds = featd[[i]]$spIdx,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	579 nSpectra = nrow(featd[[i]]),
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	580 nFiles = length(unlist(fls))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	581 )
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	582 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	583 featd <- do.call(rbind, featd)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	584 featd$spectrum <- 1:nrow(featd)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	585 ## experimentData
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	586 expdata <- lapply(x, function(z) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	587 ed <- z@experimentData
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	588 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	589 instrumentModel = ed@instrumentModel,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	590 ionSource = ed@ionSource,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	591 analyser = ed@analyser,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	592 detectorType = ed@detectorType,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	593 stringsAsFactors = FALSE)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	594 })
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	595 expdata <- do.call(rbind, expdata)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	596 expdata <- new("MIAPE",
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	597 instrumentManufacturer = expdata$instrumentManufacturer,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	598 instrumentModel = expdata$instrumentModel,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	599 ionSource = expdata$ionSource,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	600 analyser = expdata$analyser,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	601 detectorType = expdata$detectorType)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	602
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	603 ## protocolData
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	604 protodata <- lapply(x, function(z) z@protocolData)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	605 if (any(unlist(lapply(protodata, nrow)) > 0))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	606 warning("Found non-empty protocol data, but merging protocol data is",
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	607 " currently not supported. Skipped.")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	608 ## phenoData
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	609 pdata <- do.call(rbind, lapply(x, pData))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	610 res <- new(
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	611 "OnDiskMSnExp",
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	612 phenoData = new("NAnnotatedDataFrame", data = pdata),
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	613 featureData = new("AnnotatedDataFrame", featd),
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	614 processingData = new("MSnProcess",
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	615 processing = paste0("Concatenated [", date(), "]"),
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	616 files = unlist(fls), smoothed = NA),
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	617 experimentData = expdata,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	618 spectraProcessingQueue = new_procQ)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	619 if (validObject(res))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	620 res
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	621 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	622
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	623 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	624 # https://github.com/sneumann/xcms/issues/247
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	625 c.XCMSnExp <- function(...) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	626 .concatenate_XCMSnExp(...)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	627 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	628
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	629 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	630 # https://github.com/sneumann/xcms/issues/247
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	631 c.MSnbase <- function(...) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	632 .concatenate_OnDiskMSnExp(...)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	633 }

Mercurial > repos > lecorguille > msnbase_readmsdata

annotate lib.r @ 0:24f7d4e5c186 draft