| Previous changeset 3:10f7b1548200 (2018-11-09) Next changeset 5:45a1db23a4a5 (2019-03-07) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639 |
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modified:
README.rst lib.r macros_xcms.xml xcms_export_samplemetadata.r xcms_export_samplemetadata.xml |
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removed:
lib-xcms3.x.x.r |
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| diff -r 10f7b1548200 -r 8c62030a1136 README.rst --- a/README.rst Fri Nov 09 15:20:18 2018 -0500 +++ b/README.rst Mon Feb 11 06:16:45 2019 -0500 |
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| @@ -2,6 +2,10 @@ Changelog/News -------------- +**Version 3.4.3.0 - 08/02/2019** + +- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.3 + **Version 3.0.0.0 - 08/03/2018** - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods |
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| diff -r 10f7b1548200 -r 8c62030a1136 lib-xcms3.x.x.r --- a/lib-xcms3.x.x.r Fri Nov 09 15:20:18 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,152 +0,0 @@ - - -#@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(...) -} |
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| diff -r 10f7b1548200 -r 8c62030a1136 lib.r --- a/lib.r Fri Nov 09 15:20:18 2018 -0500 +++ b/lib.r Mon Feb 11 06:16:45 2019 -0500 |
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| @@ -144,7 +144,7 @@ #@author G. Le Corguille # Draw the plotChromPeakDensity 3 per page in a pdf file -getPlotChromPeakDensity <- function(xdata, mzdigit=4) { +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)) @@ -156,7 +156,7 @@ 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))) + plotChromPeakDensity(xdata, param = param, 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) } @@ -189,10 +189,10 @@ 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=groupnamesW4M(xdata), dataMatrix) + dataMatrix = cbind(name=groupnames(xdata), dataMatrix) variableMetadata <- featureDefinitions(xdata) colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt" - variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata) + variableMetadata = data.frame(name=groupnames(xdata), variableMetadata) variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute) variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) |
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| diff -r 10f7b1548200 -r 8c62030a1136 macros_xcms.xml --- a/macros_xcms.xml Fri Nov 09 15:20:18 2018 -0500 +++ b/macros_xcms.xml Mon Feb 11 06:16:45 2019 -0500 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">3.0.0</token> + <token name="@WRAPPER_VERSION@">3.4.3</token> <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</requirement> |
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| diff -r 10f7b1548200 -r 8c62030a1136 xcms_export_samplemetadata.r --- a/xcms_export_samplemetadata.r Fri Nov 09 15:20:18 2018 -0500 +++ b/xcms_export_samplemetadata.r Mon Feb 11 06:16:45 2019 -0500 |
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| @@ -3,7 +3,6 @@ #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") loadAndDisplayPackages(pkgs) |
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| diff -r 10f7b1548200 -r 8c62030a1136 xcms_export_samplemetadata.xml --- a/xcms_export_samplemetadata.xml Fri Nov 09 15:20:18 2018 -0500 +++ b/xcms_export_samplemetadata.xml Mon Feb 11 06:16:45 2019 -0500 |
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| @@ -117,6 +117,10 @@ Changelog/News -------------- +**Version 3.4.3.0 - 08/02/2019** + +- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.3 + **Version 3.0.0.0 - 09/10/2018** - NEW: a new tool to generate a sampleMetadata file you will be able to complete |