# HG changeset patch
# User workflow4metabolomics
# Date 1623915775 0
# Node ID eb115eb8f25c989fcfa06662cf962cb2f29fe371
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
diff -r 000000000000 -r eb115eb8f25c README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Thu Jun 17 07:42:55 2021 +0000
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+
+Changelog/News
+--------------
+
+.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
+
+**Version 3.12.0.0 - 08/02/2021**
+
+- NEW: first version of tool wrapper
+
diff -r 000000000000 -r eb115eb8f25c abims_xcms_refine.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/abims_xcms_refine.xml Thu Jun 17 07:42:55 2021 +0000
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+
+ Remove or merge chromatographic peaks based on specific criteria.
+
+
+ macros.xml
+ macros_xcms.xml
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+ 10.5281/zenodo.3909299
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+ 10.1021/ac051437y
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+
diff -r 000000000000 -r eb115eb8f25c lib.r
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lib.r Thu Jun 17 07:42:55 2021 +0000
@@ -0,0 +1,451 @@
+#@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
+ md5sumList <- NULL
+ for (image in args$images) {
+
+ load(image)
+ # Handle infiles
+ if (!exists("singlefile")) singlefile <- NULL
+ if (!exists("zipfile")) zipfile <- NULL
+ rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
+ zipfile <- rawFilePath$zipfile
+ singlefile <- rawFilePath$singlefile
+
+ if (exists("raw_data")) xdata <- raw_data
+ if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
+
+ cat(sampleNamesList$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 <- xcms:::.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, param = NULL, mzdigit = 4) {
+ pdf(file = "plotChromPeakDensity.pdf", width = 16, height = 12)
+
+ par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
+
+ if (length(unique(xdata$sample_group)) < 10) {
+ group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+ }else{
+ group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
+ }
+ names(group_colors) <- unique(xdata$sample_group)
+ col_per_samp <- as.character(xdata$sample_group)
+ for (i in seq_len(length(group_colors))) {
+ col_per_samp[col_per_samp == (names(group_colors)[i])] <- group_colors[i]
+ }
+
+ xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
+ for (i in seq_len(nrow(featureDefinitions(xdata)))) {
+ mzmin <- featureDefinitions(xdata)[i, ]$mzmin
+ mzmax <- featureDefinitions(xdata)[i, ]$mzmax
+ plotChromPeakDensity(xdata, param = param, mz = c(mzmin, mzmax), col = col_per_samp, pch = 16, xlim = xlim, main = paste(round(mzmin, mzdigit), round(mzmax, mzdigit)))
+ legend("topright", legend = names(group_colors), col = group_colors, cex = 0.8, lty = 1)
+ }
+
+ dev.off()
+}
+
+#@author G. Le Corguille
+# Draw the plotChromPeakDensity 3 per page in a pdf file
+getPlotAdjustedRtime <- function(xdata) {
+
+ pdf(file = "raw_vs_adjusted_rt.pdf", width = 16, height = 12)
+
+ # Color by group
+ if (length(unique(xdata$sample_group)) < 10) {
+ group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+ } else {
+ group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
+ }
+ 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, sampleNamesList) {
+ dataMatrix <- featureValues(xdata, method = "medret", value = intval)
+ colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
+ dataMatrix <- cbind(name = groupnames(xdata), dataMatrix)
+ variableMetadata <- featureDefinitions(xdata)
+ colnames(variableMetadata)[1] <- "mz"; colnames(variableMetadata)[4] <- "rt"
+ variableMetadata <- data.frame(name = groupnames(xdata), variableMetadata)
+
+ variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
+ variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
+ dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
+
+ # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
+ variableMetadata[, "peakidx"] <- vapply(variableMetadata[, "peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
+
+ 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
+ if (length(unique(xdata$sample_group)) < 10) {
+ group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
+ }else{
+ group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette = "Dark 3")
+ }
+ if (length(group_colors) > 1) {
+ names(group_colors) <- unique(xdata$sample_group)
+ plot(chrom, col = group_colors[chrom$sample_group], main = main, peakType = "none")
+ 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$sample_name)), main = main, peakType = "none")
+ legend("topright", legend = xdata@phenoData@data$sample_name, col = rainbow(length(xdata@phenoData@data$sample_name)), cex = 0.8, lty = 1)
+
+ dev.off()
+}
+
+
+# Get the polarities from all the samples of a condition
+#@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
+#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
+getSampleMetadata <- function(xdata = NULL, sampleMetadataOutput = "sampleMetadata.tsv") {
+ cat("Creating the sampleMetadata file...\n")
+
+ #Create the sampleMetada dataframe
+ sampleMetadata <- xdata@phenoData@data
+ rownames(sampleMetadata) <- NULL
+ colnames(sampleMetadata) <- c("sample_name", "class")
+
+ sampleNamesOrigin <- sampleMetadata$sample_name
+ 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$sample_name <- sampleNamesMakeNames
+
+
+ #For each sample file, the following actions are done
+ for (fileIdx in seq_len(length(fileNames(xdata)))) {
+ #Check if the file is in the CDF format
+ if (!mzR:::netCDFIsFile(fileNames(xdata))) {
+
+ # If the column isn't exist, with add one filled with NA
+ if (is.null(sampleMetadata$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 will compute MD5 checksum to check the data integrity
+#@author Gildas Le Corguille lecorguille@sb-roscoff.fr
+getMd5sum <- function(files) {
+ cat("Compute md5 checksum...\n")
+ library(tools)
+ return(as.matrix(md5sum(files)))
+}
+
+# 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
+retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile, args, prefix = "") {
+
+ if (!(prefix %in% c("", "Positive", "Negative", "MS1", "MS2"))) stop("prefix must be either '', 'Positive', 'Negative', 'MS1' or 'MS2'")
+
+ # single - if the file are passed in the command arguments -> refresh singlefile
+ if (!is.null(args[[paste0("singlefile_galaxyPath", prefix)]])) {
+ singlefile_galaxyPaths <- unlist(strsplit(args[[paste0("singlefile_galaxyPath", prefix)]], "\\|"))
+ singlefile_sampleNames <- unlist(strsplit(args[[paste0("singlefile_sampleName", prefix)]], "\\|"))
+
+ singlefile <- NULL
+ for (singlefile_galaxyPath_i in seq_len(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
+ }
+ }
+ # zipfile - if the file are passed in the command arguments -> refresh zipfile
+ if (!is.null(args[[paste0("zipfile", prefix)]]))
+ zipfile <- args[[paste0("zipfile", prefix)]]
+
+ # single
+ if (!is.null(singlefile) && (length("singlefile") > 0)) {
+ files <- vector()
+ 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)
+ files <- c(files, singlefile_sampleName)
+ }
+ }
+ # zipfile
+ 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)
+ }
+ 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)$isdir]
+ directory <- "."
+ if (length(directories) == 1) directory <- directories
+
+ cat("files_root_directory\t", directory, "\n")
+
+ filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
+ filepattern <- paste(paste("\\.", filepattern, "$", 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(list(zipfile = zipfile, singlefile = singlefile, files = files))
+
+}
+
+
+# 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 eb115eb8f25c macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Jun 17 07:42:55 2021 +0000
@@ -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 eb115eb8f25c macros_xcms.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros_xcms.xml Thu Jun 17 07:42:55 2021 +0000
@@ -0,0 +1,272 @@
+
+
+
+ 3.12.0
+
+
+ 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
+.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
+
+
+
+
+**Version 3.4.4.0 - 08/02/2019**
+
+- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
+
+
+**Version 3.6.1+galaxy* - 03/09/2019**
+
+- UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
+
+
+**Version 3.12.0+galaxy* - 03/03/2020**
+
+- UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_)
+
+
+
+
+ 10.1021/ac051437y
+
+
+
+
diff -r 000000000000 -r eb115eb8f25c repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Thu Jun 17 07:42:55 2021 +0000
@@ -0,0 +1,5 @@
+
+
+
+
+
\ No newline at end of file
diff -r 000000000000 -r eb115eb8f25c test-data/faahKO-single.xset.merged.RData
Binary file test-data/faahKO-single.xset.merged.RData has changed
diff -r 000000000000 -r eb115eb8f25c test-data/faahKO_reduce.zip
Binary file test-data/faahKO_reduce.zip has changed
diff -r 000000000000 -r eb115eb8f25c test-data/ko15.CDF
Binary file test-data/ko15.CDF has changed
diff -r 000000000000 -r eb115eb8f25c test-data/ko16.CDF
Binary file test-data/ko16.CDF has changed
diff -r 000000000000 -r eb115eb8f25c test-data/wt15.CDF
Binary file test-data/wt15.CDF has changed
diff -r 000000000000 -r eb115eb8f25c test-data/wt16.CDF
Binary file test-data/wt16.CDF has changed
diff -r 000000000000 -r eb115eb8f25c xcms_refine.r
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_refine.r Thu Jun 17 07:42:55 2021 +0000
@@ -0,0 +1,126 @@
+#!/usr/bin/env Rscript
+
+# ----- LOG FILE -----
+log_file <- file("log.txt", open = "wt")
+sink(log_file)
+sink(log_file, type = "output")
+
+
+# ----- 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")
+
+pkgs <- c("xcms", "batch", "RColorBrewer")
+loadAndDisplayPackages(pkgs)
+cat("\n\n");
+
+# ----- ARGUMENTS -----
+cat("\tARGUMENTS INFO\n")
+# interpretation of arguments given in command line as an R list of objects
+args <- parseCommandArgs(evaluate = FALSE)
+write.table(as.matrix(args), col.names = F, quote = F, sep = "\t")
+
+cat("\n\n")
+
+# ----- PROCESSING INFILE -----
+cat("\tARGUMENTS PROCESSING INFO\n")
+
+#saving the specific parameters
+args_method <- args$method
+args_image <- args$image
+args_msLevel <- args$msLevel
+param_args <- list()
+
+if (args_method == "CleanPeaks") {
+ param_args$maxPeakwidth <- args$maxPeakwidth
+} else if (args_method == "FilterIntensity") {
+ param_args$threshold <- args$threshold
+ param_args$value <- args$value
+ param_args$nValues <- args$nValues
+} else if (args_method == "MergeNeighboringPeaks") {
+ param_args$expandRt <- args$expandRt
+ param_args$expandMz <- args$expandMz
+ param_args$ppm <- args$ppm
+ param_args$minProp <- args$minProp
+}
+
+cat("\n\n")
+
+
+# ----- ARGUMENTS PROCESSING -----
+cat("\tINFILE PROCESSING INFO\n")
+
+#image is an .RData file necessary to use xset variable given by previous tools
+load(args_image)
+if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. Such RData as this might have been created by an old version of XMCS 2.*")
+
+# Handle infiles
+if (!exists("singlefile")) singlefile <- NULL
+if (!exists("zipfile")) zipfile <- NULL
+rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
+zipfile <- rawFilePath$zipfile
+singlefile <- rawFilePath$singlefile
+
+cat("\n\n")
+
+
+# ----- MAIN PROCESSING INFO -----
+cat("\tMAIN PROCESSING INFO\n")
+
+
+cat("\t\tPREPARE PARAMETERS\n\n")
+
+if (args_method == "CleanPeaks") {
+ refineChromPeaksParam <- CleanPeaksParam(maxPeakwidth = param_args$maxPeakwidth)
+} else if (args_method == "FilterIntensity") {
+ refineChromPeaksParam <- FilterIntensityParam(
+ threshold = param_args$threshold,
+ nValues = param_args$nValues,
+ value = param_args$value
+ )
+} else if (args_method == "MergeNeighboringPeaks") {
+ refineChromPeaksParam <- MergeNeighboringPeaksParam(
+ expandRt = param_args$expandRt,
+ expandMz = param_args$expandMz,
+ ppm = param_args$ppm,
+ minProp = param_args$minProp
+ )
+}
+
+cat(str(refineChromPeaksParam))
+
+cat("\n\n\t\tCOMPUTE\n")
+
+xdata <- updateObject(xdata)
+
+xdata <- refineChromPeaks(xdata, param = refineChromPeaksParam)
+
+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")
+
+#saving R data in .Rdata file to save the variables used in the present tool
+objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
+save(list = objects2save[objects2save %in% ls()], file = "xcmsSet.RData")
+
+cat("\n\n")
+
+
+cat("\tDONE\n")