| Previous changeset 14:4c757d1ba7b4 (2018-02-13) Next changeset 16:a2b6488ea1b9 (2018-09-19) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 |
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modified:
README.rst abims_xcms_summary.xml macros.xml static/images/xcms_summary_workflow.png test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html test-data/faahKO.xset.group.retcor.group.fillpeaks.summary.html xcms_summary.r |
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added:
lib-xcms3.x.x.r lib.r macros_xcms.xml |
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| diff -r 4c757d1ba7b4 -r 97ca0321931b README.rst --- a/README.rst Tue Feb 13 04:51:37 2018 -0500 +++ b/README.rst Tue Sep 18 16:14:05 2018 -0400 |
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| @@ -2,18 +2,28 @@ Changelog/News -------------- +**Version 3.0.0.0 - 14/02/2018** + +- UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods + +- IMPROVEMENT: the tool now shows all the parameters and not only those which were setted. + + **Version 1.0.4 - 13/02/2018** - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0 + **Version 1.0.3 - 03/02/2017** - IMPROVEMENT: xcms.summary can deal with merged individual data + **Version 1.0.2 - 06/07/2016** - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 + **Version 1.0.1 - 04/04/2016** - TEST: refactoring to pass planemo test using conda dependencies @@ -22,5 +32,3 @@ **Version 1.0.0 - 10/02/2016** - NEW: Create a summary of XCMS analysis - - |
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| diff -r 4c757d1ba7b4 -r 97ca0321931b abims_xcms_summary.xml --- a/abims_xcms_summary.xml Tue Feb 13 04:51:37 2018 -0500 +++ b/abims_xcms_summary.xml Tue Sep 18 16:14:05 2018 -0400 |
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| @@ -1,20 +1,20 @@ -<tool id="abims_xcms_summary" name="xcms.summary" version="1.0.4"> +<tool id="abims_xcms_summary" name="xcms process history" version="@WRAPPER_VERSION@.0"> <description>Create a summary of XCMS analysis</description> <macros> <import>macros.xml</import> + <import>macros_xcms.xml</import> </macros> - <requirements> + <expand macro="requirements"> <requirement type="package" version="1.32.0">bioconductor-camera</requirement> - <requirement type="package" version="1.1_4">r-batch</requirement> - </requirements> + </expand> <expand macro="stdio"/> <command><![CDATA[ - $__tool_directory__/xcms_summary.r + @COMMAND_RSCRIPT@/xcms_summary.r image '$image' htmlOutput '$htmlOutput' @@ -24,7 +24,7 @@ <inputs> - <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, group, retcor, fillpeaks etc.)" /> + <param name="image" type="data" format="rdata.xcms.findchrompeaks,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, group, retcor, fillpeaks etc.)" /> </inputs> @@ -33,12 +33,12 @@ </outputs> <tests> - <test> - <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" /> + <!--<test> + <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" ftype="rdata"/> <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" /> - </test> + </test>--> <test> - <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" /> + <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" ftype="rdata"/> <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" /> </test> </tests> @@ -47,9 +47,9 @@ @HELP_AUTHORS@ -============ -Xcms.summary -============ +==================== +xcms process history +==================== ----------- Description @@ -63,19 +63,19 @@ **Upstream tools** -========================= ================= ===================== ========== -Name output file format parameter -========================= ================= ===================== ========== -xcms.xcmsSet xset.RData rdata.xcms.raw RData file -------------------------- ----------------- --------------------- ---------- -xcms.group xset.RData rdata.xcms.group RData file -------------------------- ----------------- --------------------- ---------- -xcms.retcor xset.RData rdata.xcms.retcor RData file -------------------------- ----------------- --------------------- ---------- -xcms.fillpeaks xset.RData rdata.xcms.fillpeaks RData file -------------------------- ----------------- --------------------- ---------- -CAMERA.annotate xset.RData rdata.camera.* RData file -========================= ================= ===================== ========== +========================= =========================== ================================ +Name Output file Format +========================= =========================== ================================ +xcms.findChromPeaks xset.RData rdata.xcms.findchrompeaks +------------------------- --------------------------- -------------------------------- +xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group +------------------------- --------------------------- -------------------------------- +xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor +------------------------- --------------------------- -------------------------------- +xcms.fillChromPeaks ``*``.fillChromPeaks.RData rdata.xcms.fillpeaks +------------------------- --------------------------- -------------------------------- +CAMERA.annotate ``*``.annotate.*.RData rdata.camera.``*`` +========================= =========================== ================================ .. image:: xcms_summary_workflow.png @@ -85,18 +85,28 @@ Changelog/News -------------- +**Version 3.0.0.0 - 14/02/2018** + +- UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods + +- IMPROVEMENT: the tool now shows all the parameters and not only those which were set. + + **Version 1.0.4 - 13/02/2018** - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0 + **Version 1.0.3 - 03/02/2017** - IMPROVEMENT: xcms.summary can deal with merged individual data + **Version 1.0.2 - 06/07/2016** - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 + **Version 1.0.1 - 04/04/2016** - TEST: refactoring to pass planemo test using conda dependencies |
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| diff -r 4c757d1ba7b4 -r 97ca0321931b lib-xcms3.x.x.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib-xcms3.x.x.r Tue Sep 18 16:14:05 2018 -0400 |
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| @@ -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(...) +} |
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| diff -r 4c757d1ba7b4 -r 97ca0321931b lib.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib.r Tue Sep 18 16:14:05 2018 -0400 |
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| b'@@ -0,0 +1,510 @@\n+#@authors ABiMS TEAM, Y. Guitton\n+# lib.r for Galaxy Workflow4Metabolomics xcms tools\n+\n+#@author G. Le Corguille\n+# solve an issue with batch if arguments are logical TRUE/FALSE\n+parseCommandArgs <- function(...) {\n+ args <- batch::parseCommandArgs(...)\n+ for (key in names(args)) {\n+ if (args[key] %in% c("TRUE","FALSE"))\n+ args[key] = as.logical(args[key])\n+ }\n+ return(args)\n+}\n+\n+#@author G. Le Corguille\n+# This function will\n+# - load the packages\n+# - display the sessionInfo\n+loadAndDisplayPackages <- function(pkgs) {\n+ for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))\n+\n+ sessioninfo = sessionInfo()\n+ cat(sessioninfo$R.version$version.string,"\\n")\n+ cat("Main packages:\\n")\n+ for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\\t") }; cat("\\n")\n+ cat("Other loaded packages:\\n")\n+ for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\\t") }; cat("\\n")\n+}\n+\n+#@author G. Le Corguille\n+# This function merge several chromBPI or chromTIC into one.\n+mergeChrom <- function(chrom_merged, chrom) {\n+ if (is.null(chrom_merged)) return(NULL)\n+ chrom_merged@.Data <- cbind(chrom_merged@.Data, chrom@.Data)\n+ return(chrom_merged)\n+}\n+\n+#@author G. Le Corguille\n+# This function merge several xdata into one.\n+mergeXData <- function(args) {\n+ chromTIC <- NULL\n+ chromBPI <- NULL\n+ chromTIC_adjusted <- NULL\n+ chromBPI_adjusted <- NULL\n+ for(image in args$images) {\n+\n+ load(image)\n+ # Handle infiles\n+ if (!exists("singlefile")) singlefile <- NULL\n+ if (!exists("zipfile")) zipfile <- NULL\n+ rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)\n+ zipfile <- rawFilePath$zipfile\n+ singlefile <- rawFilePath$singlefile\n+ retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)\n+\n+ if (exists("raw_data")) xdata <- raw_data\n+ 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.*")\n+\n+ cat(sampleNamesList$sampleNamesOrigin,"\\n")\n+\n+ if (!exists("xdata_merged")) {\n+ xdata_merged <- xdata\n+ singlefile_merged <- singlefile\n+ md5sumList_merged <- md5sumList\n+ sampleNamesList_merged <- sampleNamesList\n+ chromTIC_merged <- chromTIC\n+ chromBPI_merged <- chromBPI\n+ chromTIC_adjusted_merged <- chromTIC_adjusted\n+ chromBPI_adjusted_merged <- chromBPI_adjusted\n+ } else {\n+ if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged,xdata)\n+ else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- .concatenate_OnDiskMSnExp(xdata_merged,xdata)\n+ else stop("\\n\\nERROR: The RData either a OnDiskMSnExp object called raw_data or a XCMSnExp object called xdata")\n+\n+ singlefile_merged <- c(singlefile_merged,singlefile)\n+ md5sumList_merged$origin <- rbind(md5sumList_merged$origin,md5sumList$origin)\n+ sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin,sampleNamesList$sampleNamesOrigin)\n+ sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames,sampleNamesList$sampleNamesMakeNames)\n+ chromTIC_merged <- mergeChrom(chromTIC_merged, chromTIC)\n+ chromBPI_merged <- mergeChrom(chromBPI_merged, chromBPI)\n+ chromTIC_adjusted_merged <- mergeChrom(chromTIC_adjusted_merged, chromTIC_adjusted)\n+ chromBPI_adjusted_merged <- mergeChrom(chromBPI_adjusted_merged, chromBPI_adjusted)\n+ }\n+ }\n+ rm(image)\n+ xdata <- xdata_merged; rm(xdata_merged)\n+ singlefile <- singlefile_merged; rm(singlefile_merged)\n+ md5sumList <- md5sumList_merged; rm(md5sumList_merged)\n+ sampleNa'..b'(files)))\n+}\n+\n+\n+# This function get the raw file path from the arguments\n+#@author Gildas Le Corguille lecorguille@sb-roscoff.fr\n+getRawfilePathFromArguments <- function(singlefile, zipfile, args, prefix="") {\n+ if (!(prefix %in% c("","Positive","Negative","MS1","MS2"))) stop("prefix must be either \'\', \'Positive\', \'Negative\', \'MS1\' or \'MS2\'")\n+\n+ if (!is.null(args[[paste0("zipfile",prefix)]])) zipfile <- args[[paste0("zipfile",prefix)]]\n+\n+ if (!is.null(args[[paste0("singlefile_galaxyPath",prefix)]])) {\n+ singlefile_galaxyPaths <- args[[paste0("singlefile_galaxyPath",prefix)]]\n+ singlefile_sampleNames <- args[[paste0("singlefile_sampleName",prefix)]]\n+ }\n+ if (exists("singlefile_galaxyPaths")){\n+ singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\\\|"))\n+ singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\\\|"))\n+\n+ singlefile <- NULL\n+ for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {\n+ singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]\n+ singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]\n+ # In case, an url is used to import data within Galaxy\n+ singlefile_sampleName <- tail(unlist(strsplit(singlefile_sampleName,"/")), n=1)\n+ singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath\n+ }\n+ }\n+ return(list(zipfile=zipfile, singlefile=singlefile))\n+}\n+\n+# This function retrieve the raw file in the working directory\n+# - if zipfile: unzip the file with its directory tree\n+# - if singlefiles: set symlink with the good filename\n+#@author Gildas Le Corguille lecorguille@sb-roscoff.fr\n+retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {\n+ if(!is.null(singlefile) && (length("singlefile")>0)) {\n+ for (singlefile_sampleName in names(singlefile)) {\n+ singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]\n+ if(!file.exists(singlefile_galaxyPath)){\n+ error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")\n+ print(error_message); stop(error_message)\n+ }\n+\n+ if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))\n+ file.copy(singlefile_galaxyPath, singlefile_sampleName)\n+\n+ }\n+ directory <- "."\n+\n+ }\n+ if(!is.null(zipfile) && (zipfile != "")) {\n+ if(!file.exists(zipfile)){\n+ error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")\n+ print(error_message)\n+ stop(error_message)\n+ }\n+\n+ #list all file in the zip file\n+ #zip_files <- unzip(zipfile,list=T)[,"Name"]\n+\n+ #unzip\n+ suppressWarnings(unzip(zipfile, unzip="unzip"))\n+\n+ #get the directory name\n+ suppressWarnings(filesInZip <- unzip(zipfile, list=T))\n+ directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))\n+ directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]\n+ directory <- "."\n+ if (length(directories) == 1) directory <- directories\n+\n+ cat("files_root_directory\\t",directory,"\\n")\n+\n+ }\n+ return (directory)\n+}\n+\n+\n+# This function retrieve a xset like object\n+#@author Gildas Le Corguille lecorguille@sb-roscoff.fr\n+getxcmsSetObject <- function(xobject) {\n+ # XCMS 1.x\n+ if (class(xobject) == "xcmsSet")\n+ return (xobject)\n+ # XCMS 3.x\n+ if (class(xobject) == "XCMSnExp") {\n+ # Get the legacy xcmsSet object\n+ suppressWarnings(xset <- as(xobject, \'xcmsSet\'))\n+ if (!is.null(xset@phenoData$sample_group))\n+ sampclass(xset) <- xset@phenoData$sample_group\n+ else\n+ sampclass(xset) <- "."\n+ return (xset)\n+ }\n+}\n' |
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| diff -r 4c757d1ba7b4 -r 97ca0321931b macros.xml --- a/macros.xml Tue Feb 13 04:51:37 2018 -0500 +++ b/macros.xml Tue Sep 18 16:14:05 2018 -0400 |
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| @@ -1,141 +1,52 @@ <?xml version="1.0"?> <macros> - <xml name="requirements"> - <requirements> - <requirement type="package" version="0.4_1">r-snow</requirement> - <requirement type="package" version="1.46.0">bioconductor-xcms</requirement> - <requirement type="package" version="1.1_4">r-batch</requirement> - </requirements> - </xml> - <xml name="requirements_light"> - <requirements> - <requirement type="package" version="1.46.0">bioconductor-xcms</requirement> - </requirements> - </xml> <xml name="stdio"> <stdio> <exit_code range="1" level="fatal" /> </stdio> </xml> - <token name="@COMMAND_XCMS_SCRIPT@"> - LC_ALL=C Rscript $__tool_directory__/xcms.r - </token> + <!-- COMMAND --> + <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token> <token name="@COMMAND_LOG_EXIT@"> ; return=\$?; - mv log.txt '$log'; - cat '$log'; + cat 'log.txt'; sh -c "exit \$return" </token> - <!-- zipfile load for planemo test --> - - <token name="@COMMAND_FILE_LOAD@"> - #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 - </token> - - <xml name="input_file_load"> - <section name="file_load_section" title="Resubmit your raw dataset or your zip file"> - <conditional name="file_load_conditional"> - <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." > - <option value="no" >no need</option> - <option value="yes" >yes</option> - </param> - <when value="no"> - </when> - <when value="yes"> - <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." /> - </when> - </conditional> - </section> + <!-- INPUT_VALIDATORS --> + <xml name="input_validator_range_integer"> + <validator type="regex" message="The format is 'min,max'" >[0-9]+ *, *[0-9]+</validator> </xml> - <xml name="test_file_load_zip"> - <section name="file_load_section"> - <conditional name="file_load_conditional"> - <param name="file_load_select" value="yes" /> - <param name="input" value="faahKO_reduce.zip" ftype="zip" /> - </conditional> - </section> + <xml name="input_validator_range_float"> + <validator type="regex" message="The format is 'min,max'" >[0-9]+\.?[0-9]* *, *[0-9]+\.?[0-9]*</validator> </xml> - <xml name="test_file_load_single"> - <section name="file_load_section"> - <conditional name="file_load_conditional"> - <param name="file_load_select" value="yes" /> - <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> - </conditional> - </section> + <xml name="input_validator_list_integer"> + <validator type="regex" message="The format is '1,2,4,6'" >[0-9, ]+</validator> </xml> - <token name="@COMMAND_PEAKLIST@"> - #if $peaklist.peaklistBool - variableMetadataOutput '$variableMetadata' - dataMatrixOutput '$dataMatrix' - convertRTMinute $peaklist.convertRTMinute - numDigitsMZ $peaklist.numDigitsMZ - numDigitsRT $peaklist.numDigitsRT - intval $peaklist.intval - #end if - </token> + + <token name="@INPUT_IMAGE_LABEL@">RData file</token> + <token name="@INPUT_IMAGE_HELP@">It contains a xcms3::XCMSnExp object (named xdata)</token> - <xml name="input_peaklist"> - <conditional name="peaklist"> - <param name="peaklistBool" type="boolean" label="Get a Peak List" /> - <when value="true"> - <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/> - <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" /> - <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" /> - <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below"> - <option value="into" selected="true">into</option> - <option value="maxo">maxo</option> - <option value="intb">intb</option> - </param> - </when> - <when value="false" /> - </conditional> - </xml> - <xml name="output_peaklist" token_function=""> - <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv"> - <filter>(peaklist['peaklistBool'])</filter> - </data> - <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" > - <filter>(peaklist['peaklistBool'])</filter> - </data> - </xml> - - <token name="@HELP_AUTHORS@"> -.. 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 + <!-- MISC --> + <token name="@HELP_AUTHORS_WRAPPERS@"> .. class:: infomark -**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M] +**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. ---------------------------------------------------- - </token> - - <xml name="citation"> - <citations> - <citation type="doi">10.1021/ac051437y</citation> + <xml name="citation_w4m"> <citation type="doi">10.1093/bioinformatics/btu813</citation> - </citations> </xml> </macros> |
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| diff -r 4c757d1ba7b4 -r 97ca0321931b macros_xcms.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_xcms.xml Tue Sep 18 16:14:05 2018 -0400 |
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| b'@@ -0,0 +1,244 @@\n+<?xml version="1.0"?>\n+<macros>\n+\n+ <token name="@WRAPPER_VERSION@">3.0.0</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</requirement>\n+ <requirement type="package" version="1.1_4">r-batch</requirement>\n+ <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>\n+ <requirement type="package" version="6.0">unzip</requirement>\n+ <yield />\n+ </requirements>\n+ </xml>\n+\n+ <!-- FILE_LOAD for planemo test -->\n+ <token name="@COMMAND_FILE_LOAD@">\n+ #if $file_load_section.file_load_conditional.file_load_select == "yes":\n+ #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"):\n+ #set singlefile_galaxyPath = \'|\'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )\n+ #set singlefile_sampleName = \'|\'.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )\n+\n+ singlefile_galaxyPath \'$singlefile_galaxyPath\' singlefile_sampleName \'$singlefile_sampleName\'\n+ #else\n+ zipfile \'$file_load_section.file_load_conditional.input\'\n+ #end if\n+ #end if\n+ </token>\n+\n+ <xml name="input_file_load">\n+ <section name="file_load_section" title="Resubmit your raw dataset or your zip file">\n+ <conditional name="file_load_conditional">\n+ <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message saying that your original dataset or zip file have been deleted on the server." >\n+ <option value="no" >no need</option>\n+ <option value="yes" >yes</option>\n+ </param>\n+ <when value="no">\n+ </when>\n+ <when value="yes">\n+ <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />\n+ </when>\n+ </conditional>\n+ </section>\n+ </xml>\n+\n+ <xml name="test_file_load_zip">\n+ <section name="file_load_section">\n+ <conditional name="file_load_conditional">\n+ <param name="file_load_select" value="yes" />\n+ <param name="input" value="faahKO_reduce.zip" ftype="zip" />\n+ </conditional>\n+ </section>\n+ </xml>\n+\n+ <xml name="test_file_load_zip_sacuri">\n+ <section name="file_load_section">\n+ <conditional name="file_load_conditional">\n+ <param name="file_load_select" value="yes" />\n+ <param name="input" value="sacuri_dir_root.zip" ftype="zip" />\n+ </conditional>\n+ </section>\n+ </xml>\n+\n+ <xml name="test_file_load_single">\n+ <section name="file_load_section">\n+ <conditional name="file_load_conditional">\n+ <param name="file_load_select" value="yes" />\n+ <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />\n+ </conditional>\n+ </section>\n+ </xml>\n+\n+ <xml name="test_file_load_single_ko15">\n+ <section name="file_load_section">\n+ <conditional name="file_load_conditional">\n+ <param name="file_load_select" value="yes" />\n+ <param name="input" value="ko15.CDF" ftype="netcdf" />\n+'..b'the m/z value at the peak apex and the m/z values left and right of it</option>\n+ <option value="meanApex3">mean of the m/z value of the peak apex and the m/z values left and right of it</option>\n+ </param>\n+ <param argument="integrate" type="select" label="Integration method" >\n+ <option value="1">peak limits are found through descent on the mexican hat filtered data (more robust, but less exact)</option>\n+ <option value="2">peak limits based on real data (more accurate but prone to noise)</option>\n+ </param>\n+ <param argument="mzdiff" type="float" value="-0.001" label="Minimum difference in m/z for peaks with overlapping retention times" help="can be negative to allow overlap" />\n+ <param argument="fitgauss" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="fitgauss" help="whether or not a Gaussian should be fitted to each peak" />\n+ <param argument="noise" type="integer" value="0" label="Noise filter" help="allowing to set a minimum intensity required for centroids to be considered in the first analysis step (centroids with intensity lower than \xe2\x80\x98noise\xe2\x80\x99 are omitted from ROI detection)." />\n+ <param argument="verboseColumns" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="verbose Columns" help="whether additional peak meta data columns should be returned" />\n+ </xml>\n+\n+ <token name="@COMMAND_CENTWAVEADVROI@">\n+ #if $sectionROI.roiList:\n+ roiList \'$sectionROI.roiList\'\n+ firstBaselineCheck $sectionROI.firstBaselineCheck\n+ #if $sectionROI.roiScales != "":\n+ roiScales "c($sectionROI.roiScales)"\n+ #end if\n+ #end if\n+ </token>\n+\n+ <xml name="input_centwaveAdvROI" token_optional="true">\n+ <param argument="roiList" type="data" format="tabular" optional="@OPTIONAL@" label="List of regions-of-interest (ROI) representing detected mass traces" help="If ROIs are submitted the first analysis step is omitted and chromatographic peak detection is performed on the submitted ROIs. Each ROI is expected to have the following elements specified: \xe2\x80\x98scmin\xe2\x80\x99 (start scan index), \xe2\x80\x98scmax\xe2\x80\x99 (end scan index), \xe2\x80\x98mzmin\xe2\x80\x99 (minimum m/z), \xe2\x80\x98mzmax\xe2\x80\x99 (maximum m/z), \xe2\x80\x98length\xe2\x80\x99 (number of scans), \xe2\x80\x98intensity\xe2\x80\x99 (summed intensity)." />\n+ <param argument="firstBaselineCheck" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Is continuous data within regions of interest is checked to be above the first baseline." />\n+ <param argument="roiScales" type="text" value="" optional="true" label="Numeric vector defining the scale for each region of interest in \xe2\x80\x98roiList\xe2\x80\x99" help="Length equal to \xe2\x80\x98roiList\xe2\x80\x99 - Should be used for the centWave-wavelets (format 0.9,1,0.2)">\n+ <expand macro="input_validator_range_float"/>\n+ </param>\n+ </xml>\n+\n+ <!-- MISC -->\n+ <token name="@HELP_AUTHORS@">\n+.. class:: infomark\n+\n+**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\n+\n+@HELP_AUTHORS_WRAPPERS@\n+\n+---------------------------------------------------\n+\n+ </token>\n+\n+ <token name="@HELP_XCMS_MANUAL@">\n+\n+For details and explanations concerning all the parameters and workflow of xcms_ package, see its manual_ and this example_\n+\n+.. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html\n+.. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf\n+.. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html\n+\n+ </token>\n+\n+ <xml name="citation">\n+ <citations>\n+ <citation type="doi">10.1021/ac051437y</citation>\n+ <expand macro="citation_w4m"/>\n+ </citations>\n+ </xml>\n+</macros>\n' |
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| diff -r 4c757d1ba7b4 -r 97ca0321931b test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData |
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| diff -r 4c757d1ba7b4 -r 97ca0321931b test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html --- a/test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html Tue Feb 13 04:51:37 2018 -0500 +++ b/test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html Tue Sep 18 16:14:05 2018 -0400 |
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| @@ -17,79 +17,126 @@ <h2>Samples used:</h2> <div><table> <tr><th>sample</th><th>filename</th><th>md5sum<sup>*</sup></th></tr> -<tr> <td> ko15 </td> <td> ./ko15.CDF </td> <td> 4698c36c0b3af007faf70975c04ccf2a </td> </tr><tr> <td> ko16 </td> <td> ./ko16.CDF </td> <td> afaeed94ced3140bc042d5ab6aeb16c1 </td> </tr><tr> <td> wt15 </td> <td> ./wt15.CDF </td> <td> d58a27fad7c04ddddb0359ddc2b7ba68 </td> </tr><tr> <td> wt16 </td> <td> ./wt16.CDF </td> <td> 29654e9f8ad48c1fbe2a41b9ba578f6e </td> </tr> +<tr><td>ko15</td><td>ko15.CDF</td><td>4698c36c0b3af007faf70975c04ccf2a</td></tr><tr><td>ko16</td><td>ko16.CDF</td><td>afaeed94ced3140bc042d5ab6aeb16c1</td></tr><tr><td>wt15</td><td>wt15.CDF</td><td>d58a27fad7c04ddddb0359ddc2b7ba68</td></tr><tr><td>wt16</td><td>wt16.CDF</td><td>29654e9f8ad48c1fbe2a41b9ba578f6e</td></tr> </table> <br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process. </div> <h2>Function launched:</h2> <div><table> <tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr> -<tr><td rowspan='4'>170203-11:04:42</td><td rowspan='4'>xcmsSet</td> -<td>nSlaves</td><td>1</td></tr> -<tr><td>method</td><td>centWave</td></tr> -<tr><td>ppm</td><td>25</td></tr> -<tr><td>peakwidth</td><td>2050</td></tr> -<tr><td rowspan='4'>170203-11:05:21</td><td rowspan='4'>xcmsSet</td> -<td>nSlaves</td><td>1</td></tr> -<tr><td>method</td><td>centWave</td></tr> -<tr><td>ppm</td><td>25</td></tr> -<tr><td>peakwidth</td><td>2050</td></tr> -<tr><td rowspan='4'>170203-11:06:21</td><td rowspan='4'>xcmsSet</td> -<td>nSlaves</td><td>1</td></tr> -<tr><td>method</td><td>centWave</td></tr> -<tr><td>ppm</td><td>25</td></tr> -<tr><td>peakwidth</td><td>2050</td></tr> -<tr><td rowspan='4'>170203-11:06:59</td><td rowspan='4'>xcmsSet</td> -<td>nSlaves</td><td>1</td></tr> -<tr><td>method</td><td>centWave</td></tr> -<tr><td>ppm</td><td>25</td></tr> -<tr><td>peakwidth</td><td>2050</td></tr> -<tr><td rowspan='6'>170203-14:38:53</td><td rowspan='6'>group</td> -<td>method</td><td>density</td></tr> -<tr><td>sleep</td><td>0.001</td></tr> -<tr><td>minfrac</td><td>0.3</td></tr> -<tr><td>bw</td><td>5</td></tr> -<tr><td>mzwid</td><td>0.01</td></tr> -<tr><td>max</td><td>50</td></tr> -<tr><td rowspan='7'>170203-14:51:16</td><td rowspan='7'>retcor</td> -<td>method</td><td>peakgroups</td></tr> -<tr><td>smooth</td><td>loess</td></tr> -<tr><td>extra</td><td>1</td></tr> -<tr><td>missing</td><td>1</td></tr> -<tr><td>span</td><td>0.2</td></tr> -<tr><td>family</td><td>gaussian</td></tr> -<tr><td>plottype</td><td>deviation</td></tr> -<tr><td rowspan='6'>170203-15:27:58</td><td rowspan='6'>group</td> -<td>method</td><td>density</td></tr> -<tr><td>sleep</td><td>0.001</td></tr> -<tr><td>minfrac</td><td>0.3</td></tr> -<tr><td>bw</td><td>5</td></tr> -<tr><td>mzwid</td><td>0.01</td></tr> -<tr><td>max</td><td>50</td></tr> -<tr><td rowspan='5'>170203-15:44:50</td><td rowspan='5'>fillPeaks</td> -<td>method</td><td>chrom</td></tr> -<tr><td>convertRTMinute</td><td>FALSE</td></tr> -<tr><td>numDigitsMZ</td><td>4</td></tr> -<tr><td>numDigitsRT</td><td>1</td></tr> -<tr><td>intval</td><td>into</td></tr> +<tr><td>Wed Feb 7 11:15:25 2018</td><td>Peak detection</td><td colspan='2'><pre> +Object of class: CentWaveParam +Parameters: + ppm: 25 + peakwidth: 20, 50 + snthresh: 10 + prefilter: 3, 100 + mzCenterFun: wMean + integrate: 1 + mzdiff: -0.001 + fitgauss: FALSE + noise: 0 + verboseColumns: FALSE + roiList length: 0 + firstBaselineCheck TRUE + roiScales length: 0 +</pre></td></tr> +<tr><td>Mon Feb 12 15:31:11 2018</td><td>Peak grouping</td><td colspan='2'><pre> +Object of class: PeakDensityParam +Parameters: + sampleGroups: character of length 4 + bw: 30 + minFraction: 0.8 + minSamples: 1 + binSize: 0.25 + maxFeatures: 50 +</pre></td></tr> +<tr><td>Mon Feb 12 15:31:19 2018</td><td>Retention time correction</td><td colspan='2'><pre> +Object of class: PeakGroupsParam +Parameters: + minFraction: 0.85 + extraPeaks: 1 + smooth: loess + span: 0.2 + family: gaussian + number of peak groups: 125 +</pre></td></tr> +<tr><td>Mon Feb 12 15:31:27 2018</td><td>Peak grouping</td><td colspan='2'><pre> +Object of class: PeakDensityParam +Parameters: + sampleGroups: character of length 4 + bw: 20 + minFraction: 0.4 + minSamples: 1 + binSize: 0.25 + maxFeatures: 50 +</pre></td></tr> +<tr><td>Wed Feb 14 09:55:13 2018</td><td>Missing peak filling</td><td colspan='2'><pre> +Object of class: FillChromPeaksParam +Parameters: + expandMz: 0 + expandRt: 0 + ppm: 0 +</pre></td></tr> </table> -<br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss +<br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss </div> +<h2>Informations about the XCMSnExp object:</h2> +<div><pre> +MSn experiment data ("XCMSnExp") +Object size in memory: 1.36 Mb +- - - Spectra data - - - + MS level(s): 1 + Number of spectra: 5112 + MSn retention times: 41:33 - 75:0 minutes +- - - Processing information - - - +Concatenated [Thu Feb 8 15:36:09 2018] + MSnbase version: 2.4.2 +- - - Meta data - - - +phenoData + rowNames: ./ko15.CDF ./ko16.CDF ./wt15.CDF ./wt16.CDF + varLabels: sample_name sample_group + varMetadata: labelDescription +Loaded from: + [1] ko15.CDF... [4] wt16.CDF + Use 'fileNames(.)' to see all files. +protocolData: none +featureData + featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total) + fvarLabels: fileIdx spIdx ... spectrum (27 total) + fvarMetadata: labelDescription +experimentData: use 'experimentData(object)' +- - - xcms preprocessing - - - +Chromatographic peak detection: + method: centWave + 15230 peaks identified in 4 samples. + On average 3808 chromatographic peaks per sample. +Alignment/retention time adjustment: + method: peak groups +Correspondence: + method: chromatographic peak density + 6332 features identified. + Median mz range of features: 0 + Median rt range of features: 0 + 5979 filled peaks (on average 1494.75 per sample). +</pre></div> <h2>Informations about the xcmsSet object:</h2> <div><pre> An "xcmsSet" object with 4 samples -Time range: 2506-4484 seconds (41.8-74.7 minutes) +Time range: 2499.4-4473.6 seconds (41.7-74.6 minutes) Mass range: 200.1-600 m/z -Peaks: 32720 (about 8180 per sample) -Peak Groups: 8157 +Peaks: 15230 (about 3808 per sample) +Peak Groups: 6332 Sample classes: KO, WT -Peak picking was performed on MS1. +Feature detection: + o Peak picking performed on MS1. + o Scan range limited to 1 - 1278 Profile settings: method = bin step = 0.1 -Memory usage: 4.25 MB +Memory usage: 2.98 MB </pre></div> <h2>Citations:</h2> <div><ul> |
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| diff -r 4c757d1ba7b4 -r 97ca0321931b test-data/faahKO.xset.group.retcor.group.fillpeaks.summary.html --- a/test-data/faahKO.xset.group.retcor.group.fillpeaks.summary.html Tue Feb 13 04:51:37 2018 -0500 +++ b/test-data/faahKO.xset.group.retcor.group.fillpeaks.summary.html Tue Sep 18 16:14:05 2018 -0400 |
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| @@ -17,7 +17,7 @@ <h2>Samples used:</h2> <div><table> <tr><th>sample</th><th>filename</th><th>md5sum<sup>*</sup></th></tr> -<tr> <td> ko15 </td> <td> faahKO_reduce/KO/ko15.CDF </td> <td> 4698c36c0b3af007faf70975c04ccf2a </td> </tr><tr> <td> ko16 </td> <td> faahKO_reduce/KO/ko16.CDF </td> <td> afaeed94ced3140bc042d5ab6aeb16c1 </td> </tr><tr> <td> wt15 </td> <td> faahKO_reduce/WT/wt15.CDF </td> <td> d58a27fad7c04ddddb0359ddc2b7ba68 </td> </tr><tr> <td> wt16 </td> <td> faahKO_reduce/WT/wt16.CDF </td> <td> 29654e9f8ad48c1fbe2a41b9ba578f6e </td> </tr> +<tr><td>ko15</td><td>faahKO_reduce/KO/ko15.CDF</td><td>4698c36c0b3af007faf70975c04ccf2a</td></tr><tr><td>ko16</td><td>faahKO_reduce/KO/ko16.CDF</td><td>afaeed94ced3140bc042d5ab6aeb16c1</td></tr><tr><td>wt15</td><td>faahKO_reduce/WT/wt15.CDF</td><td>d58a27fad7c04ddddb0359ddc2b7ba68</td></tr><tr><td>wt16</td><td>faahKO_reduce/WT/wt16.CDF</td><td>29654e9f8ad48c1fbe2a41b9ba578f6e</td></tr> </table> <br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process. </div> @@ -54,7 +54,7 @@ <tr><td rowspan='1'>160421-11:50:48</td><td rowspan='1'>fillPeaks</td> <td>method</td><td>chrom</td></tr> </table> -<br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss +<br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss </div> <h2>Informations about the xcmsSet object:</h2> <div><pre> @@ -66,6 +66,7 @@ Peak Groups: 8157 Sample classes: KO, WT +Feature detection: Profile settings: method = bin step = 0.1 |
| b |
| diff -r 4c757d1ba7b4 -r 97ca0321931b xcms_summary.r --- a/xcms_summary.r Tue Feb 13 04:51:37 2018 -0500 +++ b/xcms_summary.r Tue Sep 18 16:14:05 2018 -0400 |
| [ |
| b'@@ -1,51 +1,82 @@\n #!/usr/bin/env Rscript\n-# version="1.0.0"\n-#@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABIMS TEAM\n \n \n \n # ----- ARGUMENTS BLACKLIST -----\n #xcms.r\n-argBlacklist=c("zipfile","singlefile_galaxyPath","singlefile_sampleName","xfunction","xsetRdataOutput","sampleMetadataOutput","ticspdf","bicspdf","rplotspdf")\n+argBlacklist <- c("zipfile", "singlefile_galaxyPath", "singlefile_sampleName", "xfunction", "xsetRdataOutput", "sampleMetadataOutput", "ticspdf", "bicspdf", "rplotspdf")\n #CAMERA.r\n-argBlacklist=c(argBlacklist,"dataMatrixOutput","variableMetadataOutput","new_file_path")\n+argBlacklist <- c(argBlacklist, "dataMatrixOutput", "variableMetadataOutput", "new_file_path")\n+\n \n # ----- PACKAGE -----\n+cat("\\tSESSION INFO\\n")\n \n-pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "igraph", "xcms","CAMERA","batch")\n-for(pkg in pkgs) {\n- cat(pkg,"\\n")\n- suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))\n-}\n+#Import the different functions\n+source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }\n+source_local("lib.r")\n+source_local("lib-xcms3.x.x.r")\n+\n+pkgs <- c("CAMERA","batch")\n+loadAndDisplayPackages(pkgs)\n+cat("\\n\\n");\n \n \n # ----- FUNCTION -----\n-writehtml = function(...) { cat(...,"\\n", file=htmlOutput,append = TRUE,sep="") }\n+writehtml <- function(...) { cat(...,"\\n", file=htmlOutput,append = TRUE,sep="") }\n+writeraw <- function(htmlOutput, object, open="at") {\n+ log_file <- file(htmlOutput, open = open)\n+ sink(log_file)\n+ sink(log_file, type = "output")\n+ print(object)\n+ sink()\n+ close(log_file)\n+}\n+getSampleNames <- function(xobject) {\n+ if (class(xobject) == "xcmsSet")\n+ return (sampnames(xobject))\n+ if (class(xobject) == "XCMSnExp")\n+ return (xobject@phenoData@data$sample_name)\n+}\n+getFilePaths <- function(xobject) {\n+ if (class(xobject) == "xcmsSet")\n+ return (xobject@filepaths)\n+ if (class(xobject) == "XCMSnExp")\n+ return (fileNames(xobject))\n+}\n+equalParams <- function(param1, param2) {\n+ writeraw("param1.txt", param1, open="wt")\n+ writeraw("param2.txt", param2, open="wt")\n+ return(tools::md5sum("param1.txt") == tools::md5sum("param2.txt"))\n+}\n \n \n # ----- ARGUMENTS -----\n \n-listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects\n+args <- parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects\n \n \n # ----- ARGUMENTS PROCESSING -----\n \n #image is an .RData file necessary to use xset variable given by previous tools\n-load(listArguments[["image"]]);\n+load(args$image);\n \n-htmlOutput = "summary.html"\n-if (!is.null(listArguments[["htmlOutput"]])) htmlOutput = listArguments[["htmlOutput"]];\n+htmlOutput <- "summary.html"\n+if (!is.null(args$htmlOutput)) htmlOutput = args$htmlOutput;\n \n-user_email = NULL\n-if (!is.null(listArguments[["user_email"]])) user_email = listArguments[["user_email"]];\n+user_email <- NULL\n+if (!is.null(args$user_email)) user_email = args$user_email;\n \n-# if the RData come from CAMERA\n-if (!exists("xset") & exists("xa")) xset=xa@xcmsSet\n-\n+# if the RData come from XCMS 1.x\n+if (exists("xset")) xobject <- xset\n # retrocompatability\n-if (!exists("sampleNamesList")) sampleNamesList=list("sampleNamesMakeNames"=make.names(sampnames(xset)))\n+if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(sampnames(xobject)))\n+# if the RData come from CAMERA\n+if (exists("xa")) xobject <- xa@xcmsSet\n+# if the RData come from XCMS 3.x\n+if (exists("xdata")) xobject <- xdata\n \n-if (!exists("xset")) stop("You need at least a xset or a xa object.")\n+if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.")\n \n \n \n@@ -71,37 +102,37 @@\n writehtml("<div><h1>_'..b'ome bad characters (eg: accent) were removed from your original file, the checksum have changed too.<br/>"\n }\n \n writehtml("<tr>",sampleNameHeaderHtml,"<th>filename</th>",md5sumHeaderHtml,"</tr>")\n- writehtml(paste("<tr>",sampleNameHtml,"<td>",xset@filepaths,"</td>",md5sumHtml,"</tr>"))\n+ writehtml(paste0("<tr>",sampleNameHtml,"<td>",getFilePaths(xobject),"</td>",md5sumHtml,"</tr>"))\n \n writehtml("</table>")\n writehtml(md5sumLegend)\n@@ -110,32 +141,57 @@\n writehtml("<h2>Function launched:</h2>")\n writehtml("<div><table>")\n writehtml("<tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>")\n- for(tool in names(listOFlistArguments)) {\n- listOFlistArgumentsDisplay=listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)]\n+ # XCMS 3.x\n+ if (class(xobject) == "XCMSnExp") {\n+ xcmsFunction <- NULL\n+ params <- NULL\n+ for (processHistoryItem in processHistory(xobject)) {\n+ if ((xcmsFunction == processType(processHistoryItem)) && equalParams(params, processParam(processHistoryItem)))\n+ next\n+ timestamp <- processDate(processHistoryItem)\n+ xcmsFunction <- processType(processHistoryItem)\n+ params <- processParam(processHistoryItem)\n+ writehtml("<tr><td>",timestamp,"</td><td>",xcmsFunction,"</td><td colspan=\'2\'><pre>")\n+ writeraw(htmlOutput, params)\n+ writehtml("</pre></td></tr>")\n+ }\n+ }\n+ # CAMERA and retrocompatability XCMS 1.x\n+ if (exists("listOFlistArguments")) {\n+ for(tool in names(listOFlistArguments)) {\n+ listOFlistArgumentsDisplay <- listOFlistArguments[[tool]][!(names(listOFlistArguments[[tool]]) %in% argBlacklist)]\n \n- timestamp = strsplit(tool,"_")[[1]][1]\n- xcmsFunction = strsplit(tool,"_")[[1]][2]\n- writehtml("<tr><td rowspan=\'",length(listOFlistArgumentsDisplay),"\'>",timestamp,"</td><td rowspan=\'",length(listOFlistArgumentsDisplay),"\'>",xcmsFunction,"</td>")\n- line_begin=""\n- for (arg in names(listOFlistArgumentsDisplay)) {\n- writehtml(line_begin,"<td>",arg,"</td><td>",unlist(listOFlistArgumentsDisplay[arg][1]),"</td></tr>")\n- line_begin="<tr>"\n+ timestamp <- strsplit(tool,"_")[[1]][1]\n+ xcmsFunction <- strsplit(tool,"_")[[1]][2]\n+ writehtml("<tr><td rowspan=\'",length(listOFlistArgumentsDisplay),"\'>",timestamp,"</td><td rowspan=\'",length(listOFlistArgumentsDisplay),"\'>",xcmsFunction,"</td>")\n+ line_begin <- ""\n+ for (arg in names(listOFlistArgumentsDisplay)) {\n+ writehtml(line_begin,"<td>",arg,"</td><td>",unlist(listOFlistArgumentsDisplay[arg][1]),"</td></tr>")\n+ line_begin <- "<tr>"\n+ }\n }\n }\n writehtml("</table>")\n- writehtml("<br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss")\n+ writehtml("<br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss")\n writehtml("</div>")\n \n+ if (class(xobject) == "XCMSnExp") {\n+ writehtml("<h2>Informations about the XCMSnExp object:</h2>")\n+\n+ writehtml("<div><pre>")\n+ writeraw(htmlOutput, xobject)\n+ writehtml("</pre></div>")\n+ }\n+\n writehtml("<h2>Informations about the xcmsSet object:</h2>")\n \n writehtml("<div><pre>")\n- log_file=file(htmlOutput, open = "at")\n- sink(log_file)\n- sink(log_file, type = "output")\n- xset\n- sink()\n+ # Get the legacy xcmsSet object\n+ xset <- getxcmsSetObject(xobject)\n+ writeraw(htmlOutput, xset)\n writehtml("</pre></div>")\n \n+ # CAMERA\n if (exists("xa")) {\n writehtml("<h2>Informations about the CAMERA object:</h2>")\n \n' |
