| Previous changeset 27:bed23aa27b4b (2020-09-24) Next changeset 29:2a2850fdf29e (2023-09-11) |
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Commit message:
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" |
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modified:
README.rst abims_xcms_summary.xml lib.r macros_xcms.xml test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html xcms_summary.r |
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| diff -r bed23aa27b4b -r 018a9771de28 README.rst --- a/README.rst Thu Sep 24 08:09:02 2020 +0000 +++ b/README.rst Wed Apr 07 16:46:50 2021 +0000 |
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| @@ -4,6 +4,10 @@ .. _News: https://bioconductor.org/packages/release/bioc/news/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_) + **Version 3.6.1+galaxy1 - 05/04/2020** - UPGRADE: upgrade the CAMERA version from 1.38.0 to 1.42.0 |
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| diff -r bed23aa27b4b -r 018a9771de28 abims_xcms_summary.xml --- a/abims_xcms_summary.xml Thu Sep 24 08:09:02 2020 +0000 +++ b/abims_xcms_summary.xml Wed Apr 07 16:46:50 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="abims_xcms_summary" name="xcms process history" version="@TOOL_VERSION@+galaxy2"> +<tool id="abims_xcms_summary" name="xcms process history" version="@TOOL_VERSION@+galaxy0"> <description>Create a summary of XCMS analysis</description> @@ -8,8 +8,8 @@ </macros> <requirements> - <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement> - <requirement type="package" version="1.40.0">bioconductor-camera</requirement> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement> + <requirement type="package" version="1.46.0">bioconductor-camera</requirement> <requirement type="package" version="1.1_5">r-batch</requirement> </requirements> @@ -87,12 +87,12 @@ Changelog/News -------------- +@HELP_XCMS_NEWVERSION_31200@ + **Version 3.6.1+galaxy2 - 23/09/2020** - BUGFIX: "Error: object 'sampleNamesList' not found" in case of .RData input from CAMERA -.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS - **Version 3.6.1+galaxy1 - 05/04/2020** - UPGRADE: upgrade the CAMERA version from 1.38.0 to 1.42.0 |
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| diff -r bed23aa27b4b -r 018a9771de28 lib.r --- a/lib.r Thu Sep 24 08:09:02 2020 +0000 +++ b/lib.r Wed Apr 07 16:46:50 2021 +0000 |
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| b'@@ -6,8 +6,8 @@\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+ if (args[key] %in% c("TRUE", "FALSE"))\n+ args[key] <- as.logical(args[key])\n }\n return(args)\n }\n@@ -17,14 +17,20 @@\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+ 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+ sessioninfo <- sessionInfo()\n+ cat(sessioninfo$R.version$version.string, "\\n")\n cat("Main packages:\\n")\n- for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\\t") }; cat("\\n")\n+ for (pkg in names(sessioninfo$otherPkgs)) {\n+ cat(paste(pkg, packageVersion(pkg)), "\\t")\n+ }\n+ cat("\\n")\n cat("Other loaded packages:\\n")\n- for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\\t") }; cat("\\n")\n+ for (pkg in names(sessioninfo$loadedOnly)) {\n+ cat(paste(pkg, packageVersion(pkg)), "\\t")\n+ }\n+ cat("\\n")\n }\n \n #@author G. Le Corguille\n@@ -43,20 +49,20 @@\n chromTIC_adjusted <- NULL\n chromBPI_adjusted <- NULL\n md5sumList <- NULL\n- for(image in args$images) {\n+ for (image in args$images) {\n \n load(image)\n # Handle infiles\n if (!exists("singlefile")) singlefile <- NULL\n if (!exists("zipfile")) zipfile <- NULL\n- rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)\n+ rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)\n zipfile <- rawFilePath$zipfile\n singlefile <- rawFilePath$singlefile\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$sampleNamesOrigin,"\\n")\n+ cat(sampleNamesList$sampleNamesOrigin, "\\n")\n \n if (!exists("xdata_merged")) {\n xdata_merged <- xdata\n@@ -68,14 +74,14 @@\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 <- xcms:::.concatenate_OnDiskMSnExp(xdata_merged,xdata)\n+ if (is(xdata, "XCMSnExp")) xdata_merged <- c(xdata_merged, xdata)\n+ else if (is(xdata, "OnDiskMSnExp")) xdata_merged <- xcms:::.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$sampleNamesMakeNames)\n+ singlefile_merged <- c(singlefile_merged, singlefile)\n+ md5sumList_merged$origin <- rbind(md5sumList_merged$origin, md5sumList$origin)\n+ sampleNamesList_merged$sampleNamesOrigin <- c(sampleNamesList_merged$sampleNamesOrigin, sampleNamesList$sampleNamesOrigin)\n+ sampleNamesList_merged$sampleNamesMakeNames <- c(sampleNamesList_merged$sampleNamesMakeNames, sampleNamesList$sampleNamesMakeNam'..b'length("singlefile") > 0)) {\n files <- vector()\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+ 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+ if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = T)))\n file.copy(singlefile_galaxyPath, singlefile_sampleName)\n files <- c(files, singlefile_sampleName)\n }\n }\n # zipfile\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+ 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- suppressWarnings(unzip(zipfile, unzip="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$Name,"/"), function(x) x[1])))\n+ suppressWarnings(filesInZip <- unzip(zipfile, list = T))\n+ directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])))\n directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]\n directory <- "."\n if (length(directories) == 1) directory <- directories\n \n- cat("files_root_directory\\t",directory,"\\n")\n+ cat("files_root_directory\\t", directory, "\\n")\n \n- filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")\n- filepattern <- paste(paste("\\\\.", filepattern, "$", sep=""),collapse="|")\n+ filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")\n+ filepattern <- paste(paste("\\\\.", filepattern, "$", sep = ""), collapse = "|")\n info <- file.info(directory)\n- listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)\n+ listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)\n files <- c(directory[!info$isdir], listed)\n exists <- file.exists(files)\n files <- files[exists]\n \n }\n- return(list(zipfile=zipfile, singlefile=singlefile, files=files))\n+ return(list(zipfile = zipfile, singlefile = singlefile, files = files))\n \n }\n \n@@ -417,15 +437,15 @@\n getxcmsSetObject <- function(xobject) {\n # XCMS 1.x\n if (class(xobject) == "xcmsSet")\n- return (xobject)\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+ 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+ return(xset)\n }\n }\n' |
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| diff -r bed23aa27b4b -r 018a9771de28 macros_xcms.xml --- a/macros_xcms.xml Thu Sep 24 08:09:02 2020 +0000 +++ b/macros_xcms.xml Wed Apr 07 16:46:50 2021 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">3.6.1</token> + <token name="@TOOL_VERSION@">3.12.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement> @@ -243,6 +243,7 @@ .. _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 </token> @@ -256,6 +257,11 @@ - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_) </token> + <token name="@HELP_XCMS_NEWVERSION_31200@"> +**Version 3.12.0+galaxy* - 03/03/2020** + +- UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_) + </token> <xml name="citation"> <citations> |
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| diff -r bed23aa27b4b -r 018a9771de28 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 Thu Sep 24 08:09:02 2020 +0000 +++ b/test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html Wed Apr 07 16:46:50 2021 +0000 |
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| @@ -5,7 +5,7 @@ <title>[W4M] XCMS analysis summary</title> <style> table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; } -td,th { padding: 5px; padding-right: 12px; } +td, th { padding: 5px; padding-right: 12px; } th { background: #898989; text-align:left;color: white;} h2 { color: #FFA212; } ul li { margin-bottom:10px; } |
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| diff -r bed23aa27b4b -r 018a9771de28 xcms_summary.r --- a/xcms_summary.r Thu Sep 24 08:09:02 2020 +0000 +++ b/xcms_summary.r Wed Apr 07 16:46:50 2021 +0000 |
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| b'@@ -13,17 +13,21 @@\n cat("\\tSESSION INFO\\n")\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 <- function(fname) {\n+ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/"))\n+}\n source_local("lib.r")\n \n-pkgs <- c("CAMERA","batch")\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-writeraw <- function(htmlOutput, object, open="at") {\n+writehtml <- function(...) {\n+ cat(..., "\\n", file = htmlOutput, append = TRUE, sep = "")\n+}\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@@ -33,26 +37,26 @@\n }\n getSampleNames <- function(xobject) {\n if (class(xobject) == "xcmsSet")\n- return (sampnames(xobject))\n+ return(sampnames(xobject))\n if (class(xobject) == "XCMSnExp")\n- return (xobject@phenoData@data$sample_name)\n+ return(xobject@phenoData@data$sample_name)\n }\n getFilePaths <- function(xobject) {\n if (class(xobject) == "xcmsSet")\n- return (xobject@filepaths)\n+ return(xobject@filepaths)\n if (class(xobject) == "XCMSnExp")\n- return (fileNames(xobject))\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+ 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-args <- 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@@ -61,26 +65,26 @@\n load(args$image);\n \n htmlOutput <- "summary.html"\n-if (!is.null(args$htmlOutput)) htmlOutput = args$htmlOutput;\n+if (!is.null(args$htmlOutput)) htmlOutput <- args$htmlOutput;\n \n user_email <- NULL\n-if (!is.null(args$user_email)) user_email = args$user_email;\n+if (!is.null(args$user_email)) user_email <- args$user_email;\n \n # if the RData come from XCMS 1.x\n if (exists("xset")) {\n xobject <- xset\n # retrocompatability\n- if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(sampnames(xobject)))\n+ if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(sampnames(xobject)))\n }\n # if the RData come from CAMERA\n if (exists("xa")) {\n xobject <- xa@xcmsSet\n- if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(xa@xcmsSet@phenoData$sample_name))\n+ if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xa@xcmsSet@phenoData$sample_name))\n }\n # if the RData come from XCMS 3.x\n if (exists("xdata")) {\n xobject <- xdata\n- if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(xdata@phenoData@data$sample_name))\n+ if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames" = make.names(xdata@phenoData@data$sample_name))\n }\n \n if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.")\n@@ -97,7 +101,7 @@\n \n writehtml("<style>")\n writehtml("table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }")\n- writehtml("td,th { padding: 5px; padding-right: 12px; }")\n+ writehtml("td, th { padding: 5px; padding-right: 12px; }")\n writehtml("th { background: #898989; text-align'..b'lay[arg][1]),"</td></tr>")\n+ writehtml(line_begin, "<td>", arg, "</td><td>", unlist(listOFlistArgumentsDisplay[arg][1]), "</td></tr>")\n line_begin <- "<tr>"\n }\n }\n@@ -202,7 +206,7 @@\n writehtml("<h2>Informations about the CAMERA object:</h2>")\n \n writehtml("<div>")\n- writehtml("Number of pcgroup: ",length(xa@pspectra))\n+ writehtml("Number of pcgroup: ", length(xa@pspectra))\n writehtml("</div>")\n }\n \n@@ -210,21 +214,21 @@\n writehtml("<div><ul>")\n writehtml("<li>To cite the <b>XCMS</b> package in publications use:")\n writehtml("<ul>")\n- writehtml("<li>","Smith, C.A. and Want, E.J. and O\'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)","</li>")\n- writehtml("<li>","Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)","</li>")\n- writehtml("<li>","H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)","</li>")\n+ writehtml("<li>", "Smith, C.A. and Want, E.J. and O\'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)", "</li>")\n+ writehtml("<li>", "Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)", "</li>")\n+ writehtml("<li>", "H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)", "</li>")\n writehtml("</ul>")\n writehtml("</li>")\n \n writehtml("<li>To cite the <b>CAMERA</b> package in publications use:")\n writehtml("<ul>")\n- writehtml("<li>","Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)","</li>")\n+ writehtml("<li>", "Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)", "</li>")\n writehtml("</ul>")\n writehtml("</li>")\n \n writehtml("<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:")\n writehtml("<ul>")\n- writehtml("<li>","Franck Giacomoni, Gildas Le Corguill\xc3\xa9, Misharl Monsoor, Marion Landi, Pierre Pericard, M\xc3\xa9lanie P\xc3\xa9t\xc3\xa9ra, Christophe Duperier, Marie Tremblay-Franco, Jean-Fran\xc3\xa7ois Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Th\xc3\xa9venot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813","</li>")\n+ writehtml("<li>", "Franck Giacomoni, Gildas Le Corguill\xc3\xa9, Misharl Monsoor, Marion Landi, Pierre Pericard, M\xc3\xa9lanie P\xc3\xa9t\xc3\xa9ra, Christophe Duperier, Marie Tremblay-Franco, Jean-Fran\xc3\xa7ois Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Th\xc3\xa9venot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813", "</li>")\n writehtml("</ul>")\n writehtml("</li>")\n writehtml("</ul></div>")\n' |