msnbase_readmsdata: lib.r annotate

annotate lib.r @ 2:fa17ee3bc9ce draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty

author	lecorguille
date	Thu, 05 Apr 2018 18:04:47 -0400
parents	24f7d4e5c186
children	9581705d6578

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
2 fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	31 # This function merge several chromBPI or chromTIC into one.
fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	32 mergeChrom <- function(chromTIC_merged, chromTIC, xdata_merged) {
fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	33 if (is.null(chromTIC_merged)) return(NULL)
fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	34 chromTIC_merged@.Data <- cbind(chromTIC_merged@.Data, chromTIC@.Data)
fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	35 chromTIC_merged@phenoData <- xdata_merged@phenoData
fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	36 return(chromTIC_merged)
fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	37 }
fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	38
fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	39 #@author G. Le Corguille
0 24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	40 # This function merge several xdata into one.
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	41 mergeXData <- function(args) {
2 fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	42 chromTIC <- NULL; chromBPI <- NULL
0 24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	43 for(image in args$images) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	44 load(image)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	45 # Handle infiles
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	46 if (!exists("singlefile")) singlefile <- NULL
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	47 if (!exists("zipfile")) zipfile <- NULL
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	48 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	49 zipfile <- rawFilePath$zipfile
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	50 singlefile <- rawFilePath$singlefile
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	51 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	52 if (exists("raw_data")) xdata <- raw_data
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	53 if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	54 cat(sampleNamesList$sampleNamesOrigin,"\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	55 if (!exists("xdata_merged")) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	56 xdata_merged <- xdata
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	57 singlefile_merged <- singlefile
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	58 md5sumList_merged <- md5sumList
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	59 sampleNamesList_merged <- sampleNamesList
2 fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	60 chromTIC_merged <- chromTIC
fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	61 chromBPI_merged <- chromBPI
0 24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	62 } else {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	63 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	64 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	65 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	66 singlefile_merged <- c(singlefile_merged,singlefile)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	67 md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	68 sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	69 sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)
2 fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	70 chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC, xdata_merged)
fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	71 chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI, xdata_merged)
0 24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	72 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	73 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	74 rm(image)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	75 xdata <- xdata_merged; rm(xdata_merged)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	76 singlefile <- singlefile_merged; rm(singlefile_merged)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	77 md5sumList <- md5sumList_merged; rm(md5sumList_merged)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	78 sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged)
2 fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	79 chromTIC <- chromTIC_merged; rm(chromTIC_merged)
fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	80 chromBPI <- chromBPI_merged; rm(chromBPI_merged)
0 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 if (!is.null(args$sampleMetadata)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	83 cat("\tXSET PHENODATA SETTING...\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	84 sampleMetadataFile <- args$sampleMetadata
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	85 sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	86 xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	87
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	88 if (any(is.na(pData(xdata)$sample_group))) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	89 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	90 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	91 print(error_message)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	92 stop(error_message)
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 }
2 fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	95 return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI))
0 24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	96 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	97
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	98 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	99 # 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	100 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	101 if (convertRTMinute){
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	102 #converting the retention times (seconds) into minutes
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	103 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	104 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	105 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	106 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	107 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	108 return (variableMetadata)
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
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	111 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	112 # This function format ions identifiers
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	113 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	114 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	115 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	116 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	117 variableMetadata <- cbind(name=variableMetadata$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	118 return(variableMetadata)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	119 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	120
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	121 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	122 # 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	123 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	124 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	125
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	126 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	127
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	128 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	129 names(group_colors) <- unique(xdata$sample_group)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	130
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	131 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	132 for (i in 1:nrow(featureDefinitions(xdata))) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	133 mzmin = featureDefinitions(xdata)[i,]$mzmin
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	134 mzmax = featureDefinitions(xdata)[i,]$mzmax
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	135 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	136 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	137 }
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 dev.off()
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	140 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	141
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	142 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	143 # 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	144 getPlotAdjustedRtime <- function(xdata) {
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 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	147
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	148 # Color by group
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	149 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	150 if (length(group_colors) > 1) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	151 names(group_colors) <- unique(xdata$sample_group)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	152 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	153 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	154 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	155
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	156 # Color by sample
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	157 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	158 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	159
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	160 dev.off()
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	161 }
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 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	164 # 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	165 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	166 dataMatrix <- featureValues(xdata, method="medret", value=intval)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	167 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	168 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	169 variableMetadata <- featureDefinitions(xdata)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	170 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	171 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	172
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	173 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	174 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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 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	177 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	178
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	179 }
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 #@author G. Le Corguille
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	182 # It allow different of field separators
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	183 getDataFrameFromFile <- function(filename, header=T) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	184 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	185 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	186 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	187 if (ncol(myDataFrame) < 2) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	188 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	189 print(error_message)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	190 stop(error_message)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	191 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	192 return(myDataFrame)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	193 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	194
2 fa17ee3bc9ce planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5e066c50d2e4ac6d5796b53331cbd3198ab8c4f9-dirty lecorguille parents: 0 diff changeset	195 getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
0 24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	196
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	197 if (aggregationFun == "sum")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	198 type="Total Ion Chromatograms"
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	199 else
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	200 type="Base Peak Intensity Chromatograms"
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 adjusted="Raw"
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	203 if (hasAdjustedRtime(xdata))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	204 adjusted="Adjusted"
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	205
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	206 main <- paste(type,":",adjusted,"data")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	207
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	208 pdf(pdfname, width=16, height=10)
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 # Color by group
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	211 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	212 if (length(group_colors) > 1) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	213 names(group_colors) <- unique(xdata$sample_group)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	214 plot(chrom, col = group_colors[chrom$sample_group], main=main)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	215 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	216 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	217
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	218 # Color by sample
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	219 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	220 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	221
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	222 dev.off()
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	223 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	224
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	225
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	226 # 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	227 #@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	228 #@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	229 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	230 cat("Creating the sampleMetadata file...\n")
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 #Create the sampleMetada dataframe
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	233 sampleMetadata <- xdata@phenoData@data
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	234 rownames(sampleMetadata) <- NULL
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	235 colnames(sampleMetadata) <- c("sampleMetadata", "class")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	236
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	237 sampleNamesOrigin <- sampleMetadata$sampleMetadata
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	238 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
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 if (any(duplicated(sampleNamesMakeNames))) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	241 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	242 for (sampleName in sampleNamesOrigin) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	243 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	244 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	245 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	246 }
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 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	249 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	250 for (sampleName in sampleNamesOrigin) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	251 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	252 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	253 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	254
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	255 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	256
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 #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	259 for (fileIdx in 1:length(fileNames(xdata))) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	260 #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	261 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	262
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	263 # 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	264 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	265
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	266 #Extract the polarity (a list of polarities)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	267 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	268 #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	269 uniq_list <- unique(polarity)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	270 if (length(uniq_list)>1){
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	271 polarity <- "mixed"
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	272 } else {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	273 polarity <- as.character(uniq_list)
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 #Set the polarity attribute
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	277 sampleMetadata$polarity[fileIdx] <- polarity
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
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 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	283
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	284 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	285
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	286 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	287
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	288
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	289 # 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	290 #@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	291 checkFilesCompatibilityWithXcms <- function(directory) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	292 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	293 # WHAT XCMS WILL FIND
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	294 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	295 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	296 info <- file.info(directory)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	297 listed <- list.files(directory[info$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	298 files <- c(directory[!info$isdir], listed)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	299 files_abs <- file.path(getwd(), files)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	300 exists <- file.exists(files_abs)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	301 files[exists] <- files_abs[exists]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	302 files[exists] <- sub("//","/",files[exists])
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	303
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	304 # WHAT IS ON THE FILESYSTEM
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	305 filesystem_filepaths <- system(paste0("find \"$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	306 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	307
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	308 # COMPARISON
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	309 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	310 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	311 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	312 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	313 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	314 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	315
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	316
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	317 #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	318 #@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	319 getMSFiles <- function (directory) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	320 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	321 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	322 info <- file.info(directory)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	323 listed <- list.files(directory[info$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	324 files <- c(directory[!info$isdir], listed)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	325 exists <- file.exists(files)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	326 files <- files[exists]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	327 return(files)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	328 }
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 # 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	331 #@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	332 checkXmlStructure <- function (directory) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	333 cat("Checking XML structure...\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	334
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	335 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	336 capture <- system(cmd, intern=TRUE)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	337
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	338 if (length(capture)>0){
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	339 #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	340 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	341 write(capture, stderr())
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	342 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	343 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	344
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	345 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	346
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 # 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	349 #@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	350 deleteXmlBadCharacters<- function (directory) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	351 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	352
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	353 processed <- F
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	354 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	355 for (i in l){
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	356 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	357 capture <- suppressWarnings(system(cmd, intern=TRUE))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	358 if (length(capture)>0){
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	359 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	360 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	361 c <- system(cmd, intern=TRUE)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	362 capture <- ""
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	363 processed <- T
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 if (processed) cat("\n\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	367 return(processed)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	368 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	369
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	370
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	371 # 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	372 #@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	373 getMd5sum <- function (directory) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	374 cat("Compute md5 checksum...\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	375 # WHAT XCMS WILL FIND
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	376 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	377 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	378 info <- file.info(directory)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	379 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	380 files <- c(directory[!info$isdir], listed)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	381 exists <- file.exists(files)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	382 files <- files[exists]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	383
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	384 library(tools)
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 #cat("\n\n")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	387
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	388 return(as.matrix(md5sum(files)))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	389 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	390
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	391
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	392 # 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	393 #@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	394 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	395 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	396 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	397 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	398
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	399 if (!is.null(args$singlefile_galaxyPath)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	400 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	401 singlefile_sampleNames <- args$singlefile_sampleName
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	402 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	403 if (!is.null(args$singlefile_galaxyPathPositive)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	404 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	405 singlefile_sampleNames <- args$singlefile_sampleNamePositive
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	406 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	407 if (!is.null(args$singlefile_galaxyPathNegative)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	408 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	409 singlefile_sampleNames <- args$singlefile_sampleNameNegative
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	410 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	411 if (exists("singlefile_galaxyPaths")){
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	412 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\\|"))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	413 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\\|"))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	414
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	415 singlefile <- NULL
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	416 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	417 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	418 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	419 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
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 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	422 return(list(zipfile=zipfile, singlefile=singlefile))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	423 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	424
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	425
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	426 # 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	427 # - 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	428 # - 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	429 #@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	430 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	431 if(!is.null(singlefile) && (length("singlefile")>0)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	432 for (singlefile_sampleName in names(singlefile)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	433 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	434 if(!file.exists(singlefile_galaxyPath)){
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	435 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	436 print(error_message); stop(error_message)
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
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	439 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	440 file.copy(singlefile_galaxyPath, singlefile_sampleName)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	441
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	442 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	443 directory <- "."
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	444
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	445 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	446 if(!is.null(zipfile) && (zipfile != "")) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	447 if(!file.exists(zipfile)){
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	448 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	449 print(error_message)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	450 stop(error_message)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	451 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	452
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	453 #list all file in the zip file
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	454 #zip_files <- unzip(zipfile,list=T)[,"Name"]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	455
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	456 #unzip
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	457 suppressWarnings(unzip(zipfile, unzip="unzip"))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	458
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	459 #get the directory name
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	460 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	461 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	462 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	463 directory <- "."
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	464 if (length(directories) == 1) directory <- directories
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 cat("files_root_directory\t",directory,"\n")
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 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	469 return (directory)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	470 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	471
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	472
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	473 # This function retrieve a xset like object
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	474 #@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	475 getxcmsSetObject <- function(xobject) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	476 # XCMS 1.x
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	477 if (class(xobject) == "xcmsSet")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	478 return (xobject)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	479 # XCMS 3.x
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	480 if (class(xobject) == "XCMSnExp") {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	481 # Get the legacy xcmsSet object
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	482 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	483 sampclass(xset) <- xset@phenoData$sample_group
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	484 return (xset)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	485 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	486 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	487
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	488
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	489 #@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	490 # https://github.com/sneumann/xcms/issues/250
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	491 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	492 mzfmt <- paste("%.", mzdec, "f", sep = "")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	493 rtfmt <- paste("%.", rtdec, "f", sep = "")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	494
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	495 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	496 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), 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 if (any(dup <- duplicated(gnames)))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	499 for (dupname in unique(gnames[dup])) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	500 dupidx <- which(gnames == dupname)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	501 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	502 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	503
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	504 return (gnames)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	505 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	506
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	507 #@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	508 # https://github.com/sneumann/xcms/issues/247
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	509 .concatenate_XCMSnExp <- function(...) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	510 x <- list(...)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	511 if (length(x) == 0)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	512 return(NULL)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	513 if (length(x) == 1)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	514 return(x[[1]])
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	515 ## Check that all are XCMSnExp objects.
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	516 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	517 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	518 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	519 ## 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	520 ## them!
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	521 x <- lapply(x, function(z) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	522 if (hasAdjustedRtime(z)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	523 z <- dropAdjustedRtime(z)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	524 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	525 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	526 if (hasFeatures(z)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	527 z <- dropFeatureDefinitions(z)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	528 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	529 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	530 z
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	531 })
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	532 ## Combine peaks
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	533 fls <- lapply(x, fileNames)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	534 startidx <- cumsum(lengths(fls))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	535 pks <- lapply(x, chromPeaks)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	536 procH <- lapply(x, processHistory)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	537 for (i in 2:length(fls)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	538 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	539 procH[[i]] <- lapply(procH[[i]], function(z) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	540 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	541 z
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	542 })
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	543 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	544 pks <- do.call(rbind, pks)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	545 new_x@.processHistory <- unlist(procH)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	546 chromPeaks(new_x) <- pks
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	547 if (validObject(new_x))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	548 new_x
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	549 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	550
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	551 #@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	552 # https://github.com/sneumann/xcms/issues/247
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	553 .concatenate_OnDiskMSnExp <- function(...) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	554 x <- list(...)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	555 if (length(x) == 0)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	556 return(NULL)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	557 if (length(x) == 1)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	558 return(x[[1]])
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	559 ## Check that all are XCMSnExp objects.
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	560 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	561 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	562 ## Check processingQueue
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	563 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	564 new_procQ <- procQ[[1]]
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	565 is_ok <- unlist(lapply(procQ, function(z)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	566 !is.character(all.equal(new_procQ, z))
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 if (any(!is_ok)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	569 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	570 "Dropping the processing queue.")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	571 new_procQ <- list()
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	572 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	573 ## processingData
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	574 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	575 startidx <- cumsum(lengths(fls))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	576 ## featureData
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	577 featd <- lapply(x, fData)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	578 ## 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	579 for (i in 2:length(featd)) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	580 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	581 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	582 fileIds = featd[[i]]$fileIdx,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	583 spectrumIds = featd[[i]]$spIdx,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	584 nSpectra = nrow(featd[[i]]),
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	585 nFiles = length(unlist(fls))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	586 )
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	587 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	588 featd <- do.call(rbind, featd)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	589 featd$spectrum <- 1:nrow(featd)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	590 ## experimentData
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	591 expdata <- lapply(x, function(z) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	592 ed <- z@experimentData
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	593 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	594 instrumentModel = ed@instrumentModel,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	595 ionSource = ed@ionSource,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	596 analyser = ed@analyser,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	597 detectorType = ed@detectorType,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	598 stringsAsFactors = FALSE)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	599 })
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	600 expdata <- do.call(rbind, expdata)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	601 expdata <- new("MIAPE",
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	602 instrumentManufacturer = expdata$instrumentManufacturer,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	603 instrumentModel = expdata$instrumentModel,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	604 ionSource = expdata$ionSource,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	605 analyser = expdata$analyser,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	606 detectorType = expdata$detectorType)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	607
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	608 ## protocolData
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	609 protodata <- lapply(x, function(z) z@protocolData)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	610 if (any(unlist(lapply(protodata, nrow)) > 0))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	611 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	612 " currently not supported. Skipped.")
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	613 ## phenoData
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	614 pdata <- do.call(rbind, lapply(x, pData))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	615 res <- new(
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	616 "OnDiskMSnExp",
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	617 phenoData = new("NAnnotatedDataFrame", data = pdata),
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	618 featureData = new("AnnotatedDataFrame", featd),
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	619 processingData = new("MSnProcess",
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	620 processing = paste0("Concatenated [", date(), "]"),
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	621 files = unlist(fls), smoothed = NA),
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	622 experimentData = expdata,
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	623 spectraProcessingQueue = new_procQ)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	624 if (validObject(res))
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	625 res
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	626 }
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 #@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	629 # https://github.com/sneumann/xcms/issues/247
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	630 c.XCMSnExp <- function(...) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	631 .concatenate_XCMSnExp(...)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	632 }
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	633
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	634 #@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	635 # https://github.com/sneumann/xcms/issues/247
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	636 c.MSnbase <- function(...) {
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	637 .concatenate_OnDiskMSnExp(...)
24f7d4e5c186 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a-dirty lecorguille parents: diff changeset	638 }

Mercurial > repos > lecorguille > msnbase_readmsdata

annotate lib.r @ 2:fa17ee3bc9ce draft