# HG changeset patch # User lecorguille # Date 1537301165 14400 # Node ID c749bfd3410e7fc655fe1459f0df67ed8f0eb603 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 diff -r 000000000000 -r c749bfd3410e README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Sep 18 16:06:05 2018 -0400 @@ -0,0 +1,6 @@ +Changelog/News +-------------- + +**Version 3.0.0.0 - 07/03/2018** + +- NEW: This new tool will plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience. It will replace the one created by xcmsSet and retcor tools. diff -r 000000000000 -r c749bfd3410e lib-xcms3.x.x.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib-xcms3.x.x.r Tue Sep 18 16:06:05 2018 -0400 @@ -0,0 +1,152 @@ + + +#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 +# https://github.com/sneumann/xcms/issues/250 +groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) { + mzfmt <- paste("%.", mzdec, "f", sep = "") + rtfmt <- paste("%.", rtdec, "f", sep = "") + + gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T", + sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "") + + if (any(dup <- duplicated(gnames))) + for (dupname in unique(gnames[dup])) { + dupidx <- which(gnames == dupname) + gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_") + } + + return (gnames) +} + +#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 +# https://github.com/sneumann/xcms/issues/247 +.concatenate_XCMSnExp <- function(...) { + x <- list(...) + if (length(x) == 0) + return(NULL) + if (length(x) == 1) + return(x[[1]]) + ## Check that all are XCMSnExp objects. + if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp"))))) + stop("All passed objects should be 'XCMSnExp' objects") + new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp") + ## If any of the XCMSnExp has alignment results or detected features drop + ## them! + x <- lapply(x, function(z) { + if (hasAdjustedRtime(z)) { + z <- dropAdjustedRtime(z) + warning("Adjusted retention times found, had to drop them.") + } + if (hasFeatures(z)) { + z <- dropFeatureDefinitions(z) + warning("Feature definitions found, had to drop them.") + } + z + }) + ## Combine peaks + fls <- lapply(x, fileNames) + startidx <- cumsum(lengths(fls)) + pks <- lapply(x, chromPeaks) + procH <- lapply(x, processHistory) + for (i in 2:length(fls)) { + pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1] + procH[[i]] <- lapply(procH[[i]], function(z) { + z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1]) + z + }) + } + pks <- do.call(rbind, pks) + new_x@.processHistory <- unlist(procH) + chromPeaks(new_x) <- pks + if (validObject(new_x)) + new_x +} + +#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 +# https://github.com/sneumann/xcms/issues/247 +.concatenate_OnDiskMSnExp <- function(...) { + x <- list(...) + if (length(x) == 0) + return(NULL) + if (length(x) == 1) + return(x[[1]]) + ## Check that all are XCMSnExp objects. + if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp"))))) + stop("All passed objects should be 'OnDiskMSnExp' objects") + ## Check processingQueue + procQ <- lapply(x, function(z) z@spectraProcessingQueue) + new_procQ <- procQ[[1]] + is_ok <- unlist(lapply(procQ, function(z) + !is.character(all.equal(new_procQ, z)) + )) + if (any(!is_ok)) { + warning("Processing queues from the submitted objects differ! ", + "Dropping the processing queue.") + new_procQ <- list() + } + ## processingData + fls <- lapply(x, function(z) z@processingData@files) + startidx <- cumsum(lengths(fls)) + ## featureData + featd <- lapply(x, fData) + ## Have to update the file index and the spectrum names. + for (i in 2:length(featd)) { + featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1] + rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames( + fileIds = featd[[i]]$fileIdx, + spectrumIds = featd[[i]]$spIdx, + nSpectra = nrow(featd[[i]]), + nFiles = length(unlist(fls)) + ) + } + featd <- do.call(rbind, featd) + featd$spectrum <- 1:nrow(featd) + ## experimentData + expdata <- lapply(x, function(z) { + ed <- z@experimentData + data.frame(instrumentManufacturer = ed@instrumentManufacturer, + instrumentModel = ed@instrumentModel, + ionSource = ed@ionSource, + analyser = ed@analyser, + detectorType = ed@detectorType, + stringsAsFactors = FALSE) + }) + expdata <- do.call(rbind, expdata) + expdata <- new("MIAPE", + instrumentManufacturer = expdata$instrumentManufacturer, + instrumentModel = expdata$instrumentModel, + ionSource = expdata$ionSource, + analyser = expdata$analyser, + detectorType = expdata$detectorType) + + ## protocolData + protodata <- lapply(x, function(z) z@protocolData) + if (any(unlist(lapply(protodata, nrow)) > 0)) + warning("Found non-empty protocol data, but merging protocol data is", + " currently not supported. Skipped.") + ## phenoData + pdata <- do.call(rbind, lapply(x, pData)) + res <- new( + "OnDiskMSnExp", + phenoData = new("NAnnotatedDataFrame", data = pdata), + featureData = new("AnnotatedDataFrame", featd), + processingData = new("MSnProcess", + processing = paste0("Concatenated [", date(), "]"), + files = unlist(fls), smoothed = NA), + experimentData = expdata, + spectraProcessingQueue = new_procQ) + if (validObject(res)) + res +} + +#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 +# https://github.com/sneumann/xcms/issues/247 +c.XCMSnExp <- function(...) { + .concatenate_XCMSnExp(...) +} + +#@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7 +# https://github.com/sneumann/xcms/issues/247 +c.MSnbase <- function(...) { + .concatenate_OnDiskMSnExp(...) +} diff -r 000000000000 -r c749bfd3410e lib.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib.r Tue Sep 18 16:06:05 2018 -0400 @@ -0,0 +1,510 @@ +#@authors ABiMS TEAM, Y. Guitton +# lib.r for Galaxy Workflow4Metabolomics xcms tools + +#@author G. Le Corguille +# solve an issue with batch if arguments are logical TRUE/FALSE +parseCommandArgs <- function(...) { + args <- batch::parseCommandArgs(...) + for (key in names(args)) { + if (args[key] %in% c("TRUE","FALSE")) + args[key] = as.logical(args[key]) + } + return(args) +} + +#@author G. Le Corguille +# This function will +# - load the packages +# - display the sessionInfo +loadAndDisplayPackages <- function(pkgs) { + for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) + + sessioninfo = sessionInfo() + cat(sessioninfo$R.version$version.string,"\n") + cat("Main packages:\n") + for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") + cat("Other loaded packages:\n") + for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") +} + +#@author G. Le Corguille +# This function merge several chromBPI or chromTIC into one. +mergeChrom <- function(chrom_merged, chrom) { + if (is.null(chrom_merged)) return(NULL) + chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data) + return(chrom_merged) +} + +#@author G. Le Corguille +# This function merge several xdata into one. +mergeXData <- function(args) { + chromTIC <- NULL + chromBPI <- NULL + chromTIC_adjusted <- NULL + chromBPI_adjusted <- NULL + for(image in args$images) { + + load(image) + # Handle infiles + if (!exists("singlefile")) singlefile <- NULL + if (!exists("zipfile")) zipfile <- NULL + rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) + zipfile <- rawFilePath$zipfile + singlefile <- rawFilePath$singlefile + retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) + + if (exists("raw_data")) xdata <- raw_data + if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") + + cat(sampleNamesList$sampleNamesOrigin,"\n") + + if (!exists("xdata_merged")) { + xdata_merged <- xdata + singlefile_merged <- singlefile + md5sumList_merged <- md5sumList + sampleNamesList_merged <- sampleNamesList + chromTIC_merged <- chromTIC + chromBPI_merged <- chromBPI + chromTIC_adjusted_merged <- chromTIC_adjusted + chromBPI_adjusted_merged <- chromBPI_adjusted + } else { + if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata) + else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata) + else stop("\n\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata") + + singlefile_merged <- c(singlefile_merged,singlefile) + md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin) + sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin) + sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames) + chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC) + chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI) + chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted) + chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted) + } + } + rm(image) + xdata <- xdata_merged; rm(xdata_merged) + singlefile <- singlefile_merged; rm(singlefile_merged) + md5sumList <- md5sumList_merged; rm(md5sumList_merged) + sampleNamesList <- sampleNamesList_merged; rm(sampleNamesList_merged) + + if (!is.null(args$sampleMetadata)) { + cat("\tXSET PHENODATA SETTING...\n") + sampleMetadataFile <- args$sampleMetadata + sampleMetadata <- getDataFrameFromFile(sampleMetadataFile, header=F) + xdata@phenoData@data$sample_group=sampleMetadata$V2[match(xdata@phenoData@data$sample_name,sampleMetadata$V1)] + + if (any(is.na(pData(xdata)$sample_group))) { + sample_missing <- pData(xdata)$sample_name[is.na(pData(xdata)$sample_group)] + error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" ")) + print(error_message) + stop(error_message) + } + } + + if (!is.null(chromTIC_merged)) { chromTIC <- chromTIC_merged; chromTIC@phenoData <- xdata@phenoData } + if (!is.null(chromBPI_merged)) { chromBPI <- chromBPI_merged; chromBPI@phenoData <- xdata@phenoData } + if (!is.null(chromTIC_adjusted_merged)) { chromTIC_adjusted <- chromTIC_adjusted_merged; chromTIC_adjusted@phenoData <- xdata@phenoData } + if (!is.null(chromBPI_adjusted_merged)) { chromBPI_adjusted <- chromBPI_adjusted_merged; chromBPI_adjusted@phenoData <- xdata@phenoData } + + return(list("xdata"=xdata, "singlefile"=singlefile, "md5sumList"=md5sumList,"sampleNamesList"=sampleNamesList, "chromTIC"=chromTIC, "chromBPI"=chromBPI, "chromTIC_adjusted"=chromTIC_adjusted, "chromBPI_adjusted"=chromBPI_adjusted)) +} + +#@author G. Le Corguille +# This function convert if it is required the Retention Time in minutes +RTSecondToMinute <- function(variableMetadata, convertRTMinute) { + if (convertRTMinute){ + #converting the retention times (seconds) into minutes + print("converting the retention times into minutes in the variableMetadata") + variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60 + variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60 + variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60 + } + return (variableMetadata) +} + +#@author G. Le Corguille +# This function format ions identifiers +formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) { + splitDeco <- strsplit(as.character(variableMetadata$name),"_") + idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) }) + namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco)) + variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))]) + return(variableMetadata) +} + +#@author G. Le Corguille +# This function convert the remain NA to 0 in the dataMatrix +naTOzeroDataMatrix <- function(dataMatrix, naTOzero) { + if (naTOzero){ + dataMatrix[is.na(dataMatrix)] <- 0 + } + return (dataMatrix) +} + +#@author G. Le Corguille +# Draw the plotChromPeakDensity 3 per page in a pdf file +getPlotChromPeakDensity <- function(xdata, mzdigit=4) { + pdf(file="plotChromPeakDensity.pdf", width=16, height=12) + + par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5)) + + group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] + names(group_colors) <- unique(xdata$sample_group) + + xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax)) + for (i in 1:nrow(featureDefinitions(xdata))) { + mzmin = featureDefinitions(xdata)[i,]$mzmin + mzmax = featureDefinitions(xdata)[i,]$mzmax + plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit))) + legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) + } + + dev.off() +} + +#@author G. Le Corguille +# Draw the plotChromPeakDensity 3 per page in a pdf file +getPlotAdjustedRtime <- function(xdata) { + + pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12) + + # Color by group + group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] + if (length(group_colors) > 1) { + names(group_colors) <- unique(xdata$sample_group) + plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group]) + legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) + } + + # Color by sample + plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name))) + legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1) + + dev.off() +} + +#@author G. Le Corguille +# value: intensity values to be used into, maxo or intb +getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput) { + dataMatrix <- featureValues(xdata, method="medret", value=intval) + colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix)) + dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix) + variableMetadata <- featureDefinitions(xdata) + colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt" + variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata) + + variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute) + variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) + dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero) + + write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F) + write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F) + +} + +#@author G. Le Corguille +# It allow different of field separators +getDataFrameFromFile <- function(filename, header=T) { + myDataFrame <- read.table(filename, header=header, sep=";", stringsAsFactors=F) + if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep="\t", stringsAsFactors=F) + if (ncol(myDataFrame) < 2) myDataFrame <- read.table(filename, header=header, sep=",", stringsAsFactors=F) + if (ncol(myDataFrame) < 2) { + error_message="Your tabular file seems not well formatted. The column separators accepted are ; , and tabulation" + print(error_message) + stop(error_message) + } + return(myDataFrame) +} + +#@author G. Le Corguille +# Draw the BPI and TIC graphics +# colored by sample names or class names +getPlotChromatogram <- function(chrom, xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") { + + if (aggregationFun == "sum") + type="Total Ion Chromatograms" + else + type="Base Peak Intensity Chromatograms" + + adjusted="Raw" + if (hasAdjustedRtime(xdata)) + adjusted="Adjusted" + + main <- paste(type,":",adjusted,"data") + + pdf(pdfname, width=16, height=10) + + # Color by group + group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] + if (length(group_colors) > 1) { + names(group_colors) <- unique(xdata$sample_group) + plot(chrom, col = group_colors[chrom$sample_group], main=main) + legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) + } + + # Color by sample + plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main) + legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1) + + dev.off() +} + + +# Get the polarities from all the samples of a condition +#@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM +getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") { + cat("Creating the sampleMetadata file...\n") + + #Create the sampleMetada dataframe + sampleMetadata <- xdata@phenoData@data + rownames(sampleMetadata) <- NULL + colnames(sampleMetadata) <- c("sampleMetadata", "class") + + sampleNamesOrigin <- sampleMetadata$sampleMetadata + sampleNamesMakeNames <- make.names(sampleNamesOrigin) + + if (any(duplicated(sampleNamesMakeNames))) { + write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr()) + for (sampleName in sampleNamesOrigin) { + write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr()) + } + stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") + } + + if (!all(sampleNamesOrigin == sampleNamesMakeNames)) { + cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n") + for (sampleName in sampleNamesOrigin) { + cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n")) + } + } + + sampleMetadata$sampleMetadata <- sampleNamesMakeNames + + + #For each sample file, the following actions are done + for (fileIdx in 1:length(fileNames(xdata))) { + #Check if the file is in the CDF format + if (!mzR:::netCDFIsFile(fileNames(xdata))) { + + # If the column isn't exist, with add one filled with NA + if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA + + #Extract the polarity (a list of polarities) + polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"] + #Verify if all the scans have the same polarity + uniq_list <- unique(polarity) + if (length(uniq_list)>1){ + polarity <- "mixed" + } else { + polarity <- as.character(uniq_list) + } + + #Set the polarity attribute + sampleMetadata$polarity[fileIdx] <- polarity + } + + } + + write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput) + + return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames)) + +} + + +# This function check if xcms will found all the files +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM +checkFilesCompatibilityWithXcms <- function(directory) { + cat("Checking files filenames compatibilities with xmcs...\n") + # WHAT XCMS WILL FIND + filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") + filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") + info <- file.info(directory) + listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE) + files <- c(directory[!info$isdir], listed) + files_abs <- file.path(getwd(), files) + exists <- file.exists(files_abs) + files[exists] <- files_abs[exists] + files[exists] <- sub("//","/",files[exists]) + + # WHAT IS ON THE FILESYSTEM + filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\""), intern=T) + filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] + + # COMPARISON + if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { + write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr()) + write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr()) + stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") + } +} + + +#This function list the compatible files within the directory as xcms did +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM +getMSFiles <- function (directory) { + filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") + filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") + info <- file.info(directory) + listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE) + files <- c(directory[!info$isdir], listed) + exists <- file.exists(files) + files <- files[exists] + return(files) +} + +# This function check if XML contains special caracters. It also checks integrity and completness. +#@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM +checkXmlStructure <- function (directory) { + cat("Checking XML structure...\n") + + cmd <- paste0("IFS=$'\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 $xml;fi; done;") + capture <- system(cmd, intern=TRUE) + + if (length(capture)>0){ + #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture) + write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr()) + write(capture, stderr()) + stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files") + } + +} + + +# This function check if XML contain special characters +#@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM +deleteXmlBadCharacters<- function (directory) { + cat("Checking Non ASCII characters in the XML...\n") + + processed <- F + l <- system( paste0("find '",directory, "' -not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"), intern=TRUE) + for (i in l){ + cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="") + capture <- suppressWarnings(system(cmd, intern=TRUE)) + if (length(capture)>0){ + cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i) + print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") ) + c <- system(cmd, intern=TRUE) + capture <- "" + processed <- T + } + } + if (processed) cat("\n\n") + return(processed) +} + + +# This function will compute MD5 checksum to check the data integrity +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr +getMd5sum <- function (directory) { + cat("Compute md5 checksum...\n") + # WHAT XCMS WILL FIND + filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") + filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="|") + info <- file.info(directory) + listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE) + files <- c(directory[!info$isdir], listed) + exists <- file.exists(files) + files <- files[exists] + + library(tools) + + #cat("\n\n") + + return(as.matrix(md5sum(files))) +} + + +# This function get the raw file path from the arguments +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr +getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") { + if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'") + + if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]] + + if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) { + singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]] + singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]] + } + if (exists("singlefile_galaxyPaths")){ + singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\|")) + singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\|")) + + singlefile <- NULL + for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { + singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i] + singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i] + # In case, an url is used to import data within Galaxy + singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1) + singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath + } + } + return(list(zipfile=zipfile, singlefile=singlefile)) +} + +# This function retrieve the raw file in the working directory +# - if zipfile: unzip the file with its directory tree +# - if singlefiles: set symlink with the good filename +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr +retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) { + if(!is.null(singlefile) && (length("singlefile")>0)) { + for (singlefile_sampleName in names(singlefile)) { + singlefile_galaxyPath <- singlefile[[singlefile_sampleName]] + if(!file.exists(singlefile_galaxyPath)){ + error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") + print(error_message); stop(error_message) + } + + if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T))) + file.copy(singlefile_galaxyPath, singlefile_sampleName) + + } + directory <- "." + + } + if(!is.null(zipfile) && (zipfile != "")) { + if(!file.exists(zipfile)){ + error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") + print(error_message) + stop(error_message) + } + + #list all file in the zip file + #zip_files <- unzip(zipfile,list=T)[,"Name"] + + #unzip + suppressWarnings(unzip(zipfile, unzip="unzip")) + + #get the directory name + suppressWarnings(filesInZip <- unzip(zipfile, list=T)) + directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))) + directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] + directory <- "." + if (length(directories) == 1) directory <- directories + + cat("files_root_directory\t",directory,"\n") + + } + return (directory) +} + + +# This function retrieve a xset like object +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr +getxcmsSetObject <- function(xobject) { + # XCMS 1.x + if (class(xobject) == "xcmsSet") + return (xobject) + # XCMS 3.x + if (class(xobject) == "XCMSnExp") { + # Get the legacy xcmsSet object + suppressWarnings(xset <- as(xobject, 'xcmsSet')) + if (!is.null(xset@phenoData$sample_group)) + sampclass(xset) <- xset@phenoData$sample_group + else + sampclass(xset) <- "." + return (xset) + } +} diff -r 000000000000 -r c749bfd3410e macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Sep 18 16:06:05 2018 -0400 @@ -0,0 +1,52 @@ + + + + + + + + + + LC_ALL=C Rscript $__tool_directory__/ + + + ; + return=\$?; + cat 'log.txt'; + sh -c "exit \$return" + + + + + [0-9]+ *, *[0-9]+ + + + + [0-9]+\.?[0-9]* *, *[0-9]+\.?[0-9]* + + + + [0-9, ]+ + + + + RData file + It contains a xcms3::XCMSnExp object (named xdata) + + + + + +.. class:: infomark + +**Galaxy integration** ABiMS TEAM - SU/CNRS - Station biologique de Roscoff and Yann Guitton - LABERCA +Part of Workflow4Metabolomics.org [W4M] + + | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. + + + + + 10.1093/bioinformatics/btu813 + + diff -r 000000000000 -r c749bfd3410e macros_xcms.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_xcms.xml Tue Sep 18 16:06:05 2018 -0400 @@ -0,0 +1,244 @@ + + + + 3.0.0 + + + bioconductor-xcms + r-batch + r-rcolorbrewer + unzip + + + + + + + #if $file_load_section.file_load_conditional.file_load_select == "yes": + #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"): + #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] ) + #set singlefile_sampleName = '|'.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] ) + + singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' + #else + zipfile '$file_load_section.file_load_conditional.input' + #end if + #end if + + + +
+ + + + + + + + + + + +
+ + + +
+ + + + +
+ + + +
+ + + + +
+ + + +
+ + + + +
+ + + +
+ + + + +
+ + + + + #if $peaklist.peaklistBool + convertRTMinute $peaklist.convertRTMinute + numDigitsMZ $peaklist.numDigitsMZ + numDigitsRT $peaklist.numDigitsRT + intval $peaklist.intval + naTOzero $peaklist.naTOzero + #end if + + + + + + + + + + + + + + + + + + + + + + + (peaklist['peaklistBool']) + + + (peaklist['peaklistBool']) + + + + + +Get a Peak List +--------------- + +If 'true', the module generates two additional files corresponding to the peak list: +- the variable metadata file (corresponding to information about extracted ions such as mass or retention time) +- the data matrix (corresponding to related intensities) + +**decimal places for [mass or retention time] values in identifiers** + + | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time. + | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively. + | Theses parameters do not affect decimal places in columns other than the identifier one. + +**Reported intensity values** + + | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter: + | - into: integrated area of original (raw) peak + | - maxo: maximum intensity of original (raw) peak + | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’) + + + + +xset.variableMetadata.tsv : tabular format + + | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter** modules. + +xset.dataMatrix.tsv : tabular format + + | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter** modules. + + + + + ppm $methods.ppm + peakwidth "c($methods.peakwidth)" + + ## Advanced + snthresh $methods.CentWaveAdv.snthresh + prefilter "c($methods.CentWaveAdv.prefilter)" + mzCenterFun $methods.CentWaveAdv.mzCenterFun + integrate $methods.CentWaveAdv.integrate + mzdiff $methods.CentWaveAdv.mzdiff + fitgauss $methods.CentWaveAdv.fitgauss + noise $methods.CentWaveAdv.noise + verboseColumns $methods.CentWaveAdv.verboseColumns + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #if $sectionROI.roiList: + roiList '$sectionROI.roiList' + firstBaselineCheck $sectionROI.firstBaselineCheck + #if $sectionROI.roiScales != "": + roiScales "c($sectionROI.roiScales)" + #end if + #end if + + + + + + + + + + + + +.. class:: infomark + +**Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu + +@HELP_AUTHORS_WRAPPERS@ + +--------------------------------------------------- + + + + + +For details and explanations concerning all the parameters and workflow of xcms_ package, see its manual_ and this example_ + +.. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html +.. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf +.. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html + + + + + + 10.1021/ac051437y + + + + diff -r 000000000000 -r c749bfd3410e repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Tue Sep 18 16:06:05 2018 -0400 @@ -0,0 +1,5 @@ + + + + + diff -r 000000000000 -r c749bfd3410e static/images/xcms_plot_chromatogram_workflow.png Binary file static/images/xcms_plot_chromatogram_workflow.png has changed diff -r 000000000000 -r c749bfd3410e test-data/BPIs.pdf Binary file test-data/BPIs.pdf has changed diff -r 000000000000 -r c749bfd3410e test-data/TICs.pdf Binary file test-data/TICs.pdf has changed diff -r 000000000000 -r c749bfd3410e test-data/faahKO-single.xset.merged.group.retcor.RData Binary file test-data/faahKO-single.xset.merged.group.retcor.RData has changed diff -r 000000000000 -r c749bfd3410e test-data/ko15.CDF Binary file test-data/ko15.CDF has changed diff -r 000000000000 -r c749bfd3410e test-data/ko16.CDF Binary file test-data/ko16.CDF has changed diff -r 000000000000 -r c749bfd3410e test-data/sampleMetadata.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampleMetadata.tab Tue Sep 18 16:06:05 2018 -0400 @@ -0,0 +1,6 @@ +wt16 WT +ko16 KO +wt15 WT +ko15 KO +ko10 KO +foobar01 FOOBAR diff -r 000000000000 -r c749bfd3410e test-data/wt15.CDF Binary file test-data/wt15.CDF has changed diff -r 000000000000 -r c749bfd3410e test-data/wt16.CDF Binary file test-data/wt16.CDF has changed diff -r 000000000000 -r c749bfd3410e xcms_plot_chromatogram.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xcms_plot_chromatogram.r Tue Sep 18 16:06:05 2018 -0400 @@ -0,0 +1,76 @@ +#!/usr/bin/env Rscript + + +# ----- PACKAGE ----- +cat("\tSESSION INFO\n") + +#Import the different functions +source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } +source_local("lib.r") +source_local("lib-xcms3.x.x.r") + +pkgs <- c("xcms","batch","RColorBrewer") +loadAndDisplayPackages(pkgs) +cat("\n\n"); + + +# ----- ARGUMENTS ----- +cat("\tARGUMENTS INFO\n") +args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects +write.table(as.matrix(args), col.names=F, quote=F, sep='\t') + +cat("\n\n") + +# ----- PROCESSING INFILE ----- +cat("\tARGUMENTS PROCESSING INFO\n") + +cat("\n\n") + + +# ----- ARGUMENTS PROCESSING ----- +cat("\tINFILE PROCESSING INFO\n") + +mergeXDataReturn <- mergeXData(args) +xdata <- mergeXDataReturn$xdata +singlefile <- mergeXDataReturn$singlefile +md5sumList <- mergeXDataReturn$md5sumList +sampleNamesList <- mergeXDataReturn$sampleNamesList +chromTIC <- mergeXDataReturn$chromTIC +chromBPI <- mergeXDataReturn$chromBPI +chromTIC_adjusted <- mergeXDataReturn$chromTIC_adjusted +chromBPI_adjusted <- mergeXDataReturn$chromBPI_adjusted + +cat("\n\n") + + +# ----- MAIN PROCESSING INFO ----- +cat("\tMAIN PROCESSING INFO\n") + + +cat("\t\tDRAW GRAPHICS\n") + +if (!is.null(chromTIC) || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") } +if (!is.null(chromBPI) || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") } + +if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted +if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted + +getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum") +getPlotChromatogram(chromBPI, xdata, pdfname="BPIs.pdf", aggregationFun = "max") + +cat("\n\n") + +# ----- EXPORT ----- + +cat("\tXCMSnExp OBJECT INFO\n") +print(xdata) +cat("\n\n") + +cat("\txcmsSet OBJECT INFO\n") +# Get the legacy xcmsSet object +xset <- getxcmsSetObject(xdata) +print(xset) +cat("\n\n") + + +cat("\tDONE\n") diff -r 000000000000 -r c749bfd3410e xcms_plot_chromatogram.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xcms_plot_chromatogram.xml Tue Sep 18 16:06:05 2018 -0400 @@ -0,0 +1,113 @@ + + Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s) + + + macros.xml + macros_xcms.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +