| Previous changeset 13:226fb89cacc4 (2020-02-12) Next changeset 15:7faf9b2d83f6 (2023-09-11) |
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Commit message:
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27" |
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modified:
README.rst lib.r macros_msnbase.xml msnbase_readmsdata.r msnbase_readmsdata.xml repository_dependencies.xml |
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| diff -r 226fb89cacc4 -r 11ab2081bd4a README.rst --- a/README.rst Wed Feb 12 08:27:38 2020 -0500 +++ b/README.rst Mon Apr 12 09:35:02 2021 +0000 |
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| @@ -2,6 +2,12 @@ Changelog/News -------------- +.. _News: https://lgatto.github.io/MSnbase/news/index.html + +**Version 2.16.1+galaxy0 - 08/04/2019** + +- UPGRADE: upgrade the MSnbase version from 2.8.2 to 2.16.1 (see MSnbase News_). Almost all the new features may not concern our usage of MSnbase. + **Version 2.8.2.1 - 30/04/2019** - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms. |
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| diff -r 226fb89cacc4 -r 11ab2081bd4a lib.r --- a/lib.r Wed Feb 12 08:27:38 2020 -0500 +++ b/lib.r Mon Apr 12 09:35:02 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@@ -403,15 +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 226fb89cacc4 -r 11ab2081bd4a macros_msnbase.xml --- a/macros_msnbase.xml Wed Feb 12 08:27:38 2020 -0500 +++ b/macros_msnbase.xml Mon Apr 12 09:35:02 2021 +0000 |
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| @@ -1,10 +1,10 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">2.8.2</token> + <token name="@WRAPPER_VERSION@">2.16.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-msnbase</requirement> - <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="1.1_5">r-batch</requirement> <requirement type="package" version="6.0">unzip</requirement> <yield /> </requirements> |
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| diff -r 226fb89cacc4 -r 11ab2081bd4a msnbase_readmsdata.r --- a/msnbase_readmsdata.r Wed Feb 12 08:27:38 2020 -0500 +++ b/msnbase_readmsdata.r Mon Apr 12 09:35:02 2021 +0000 |
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| @@ -1,7 +1,7 @@ #!/usr/bin/env Rscript # ----- LOG FILE ----- -log_file <- file("log.txt", open="wt") +log_file <- file("log.txt", open = "wt") sink(log_file) sink(log_file, type = "output") @@ -10,10 +10,12 @@ 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 <- 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("MSnbase","batch") +pkgs <- c("MSnbase", "batch") loadAndDisplayPackages(pkgs) cat("\n\n"); @@ -21,7 +23,7 @@ # ----- ARGUMENTS ----- cat("\tARGUMENTS INFO\n") args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects -write.table(as.matrix(args), col.names=F, quote=F, sep='\t') +write.table(as.matrix(args), col.names = F, quote = F, sep = "\t") cat("\n\n") @@ -38,7 +40,7 @@ # Handle infiles if (!exists("singlefile")) singlefile <- NULL if (!exists("zipfile")) zipfile <- NULL -rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args) +rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) zipfile <- rawFilePath$zipfile singlefile <- rawFilePath$singlefile files <- rawFilePath$files @@ -55,23 +57,19 @@ cat("\t\tCOMPUTE\n") cat("\t\t\tCreate a phenodata data.frame\n") -s_groups <- sapply(files, function(x) tail(unlist(strsplit(dirname(x),"/")), n=1)) +s_groups <- sapply(files, function(x) tail(unlist(strsplit(dirname(x), "/")), n = 1)) s_name <- tools::file_path_sans_ext(basename(files)) -pd <- data.frame(sample_name=s_name, sample_group=s_groups, stringsAsFactors=FALSE) +pd <- data.frame(sample_name = s_name, sample_group = s_groups, stringsAsFactors = FALSE) print(pd) cat("\t\t\tLoad Raw Data\n") -raw_data <- readMSData(files=files, pdata = new("NAnnotatedDataFrame", pd), mode="onDisk") +raw_data <- readMSData(files = files, pdata = new("NAnnotatedDataFrame", pd), mode = "onDisk") # Transform the files absolute pathways into relative pathways -raw_data@processingData@files <- sub(paste(getwd(), "/", sep="") , "", raw_data@processingData@files) +raw_data@processingData@files <- sub(paste(getwd(), "/", sep = ""), "", raw_data@processingData@files) # Create a sampleMetada file -sampleNamesList <- getSampleMetadata(xdata=raw_data, sampleMetadataOutput="sampleMetadata.tsv") - -#cat("\t\t\tCompute and Store TIC and BPI\n") -#chromTIC <- chromatogram(raw_data, aggregationFun = "sum") -#chromBPI <- chromatogram(raw_data, aggregationFun = "max") +sampleNamesList <- getSampleMetadata(xdata = raw_data, sampleMetadataOutput = "sampleMetadata.tsv") cat("\n\n") @@ -85,7 +83,7 @@ #saving R data in .Rdata file to save the variables used in the present tool objects2save <- c("raw_data", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI") -save(list=objects2save[objects2save %in% ls()], file="readmsdata.RData") +save(list = objects2save[objects2save %in% ls()], file = "readmsdata.RData") cat("\tDONE\n") |
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| diff -r 226fb89cacc4 -r 11ab2081bd4a msnbase_readmsdata.xml --- a/msnbase_readmsdata.xml Wed Feb 12 08:27:38 2020 -0500 +++ b/msnbase_readmsdata.xml Mon Apr 12 09:35:02 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@.2"> +<tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@+galaxy0"> <description>Imports mass-spectrometry data files</description> <macros> @@ -47,7 +47,7 @@ <has_text text="rowNames: faahKO_reduce/KO/ko15.CDF faahKO_reduce/KO/ko16.CDF" /> <has_text text="faahKO_reduce/WT/wt15.CDF faahKO_reduce/WT/wt16.CDF" /> <has_text text="featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)" /> - <has_text text="fvarLabels: fileIdx spIdx ... spectrum (28 total)" /> + <has_text text="fvarLabels: fileIdx spIdx ... spectrum (33 total)" /> <has_text text="faahKO_reduce/KO/ko15.CDF ko15 KO" /> <has_text text="faahKO_reduce/KO/ko16.CDF ko16 KO" /> <has_text text="faahKO_reduce/WT/wt15.CDF wt15 WT" /> @@ -61,7 +61,7 @@ <has_text text="rowNames: ko15.CDF" /> <has_text text="ko15.CDF" /> <has_text text="featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)" /> - <has_text text="fvarLabels: fileIdx spIdx ... spectrum (28 total)" /> + <has_text text="fvarLabels: fileIdx spIdx ... spectrum (33 total)" /> <has_text text="ko15.CDF ko15 ." /> </assert_stdout> </test> @@ -234,7 +234,11 @@ Changelog/News -------------- -.. _News: https://bioconductor.org/packages/release/bioc/news/MSnbase/NEWS +.. _News: https://lgatto.github.io/MSnbase/news/index.html + +**Version 2.16.1+galaxy0 - 08/04/2019** + +- UPGRADE: upgrade the MSnbase version from 2.8.2 to 2.16.1 (see MSnbase News_). Almost all the new features may not concern our usage of MSnbase. **Version 2.8.2.1 - 30/04/2019** |
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| diff -r 226fb89cacc4 -r 11ab2081bd4a repository_dependencies.xml --- a/repository_dependencies.xml Wed Feb 12 08:27:38 2020 -0500 +++ b/repository_dependencies.xml Mon Apr 12 09:35:02 2021 +0000 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0" ?> <repositories> - <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/> - <repository changeset_revision="544f6d2329ac" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/> + <repository name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="7800ba9a4c1e"/> + <repository name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="544f6d2329ac"/> </repositories> \ No newline at end of file |