| Previous changeset 14:11ab2081bd4a (2021-04-12) Next changeset 16:12def6edac2f (2023-11-21) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e |
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modified:
lib.r msnbase_readmsdata.r msnbase_readmsdata.xml |
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added:
macros_xcms.xml static/images/xcms_fillpeaks_workflow.png static/images/xcms_group.png static/images/xcms_group_workflow.png static/images/xcms_merge_workflow.png static/images/xcms_plot_chromatogram_workflow.png static/images/xcms_retcor.png static/images/xcms_retcor_workflow.png static/images/xcms_summary_workflow.png static/images/xcms_tics.png static/images/xcms_xcmsset_workflow.png test-data/BPIs.pdf test-data/TICs.pdf test-data/faahKO-single-class.xset.group.retcor.group.fillPeaks.dataMatrix.NAless.tsv test-data/faahKO-single-class.xset.group.retcor.group.fillPeaks.variableMetadata.tsv test-data/faahKO-single-class.xset.merged.RData test-data/faahKO-single-class.xset.merged.group.RData test-data/faahKO-single-class.xset.merged.group.retcor.RData test-data/faahKO-single-class.xset.merged.group.retcor.group.RData test-data/faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.RData 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.dataMatrix.tsv test-data/faahKO.xset.group.variableMetadata.tsv test-data/ko15-raw.RData test-data/ko15-xset.RData test-data/ko16-raw.RData test-data/ko16-xset.RData test-data/ko16.CDF test-data/noclass.merged.sampleMetadata.tsv test-data/roiList.txt test-data/sampleMetadata.tab test-data/sampleMetadata_missing.tab test-data/wt15-raw.RData test-data/wt15-xset.RData test-data/wt15.CDF test-data/wt16-raw.RData test-data/wt16-xset.RData test-data/wt16.CDF |
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removed:
README.rst repository_dependencies.xml |
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| diff -r 11ab2081bd4a -r 7faf9b2d83f6 README.rst --- a/README.rst Mon Apr 12 09:35:02 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,21 +0,0 @@ - -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. - -**Version 2.8.2.0 - 08/04/2019** - -- UPGRADE: upgrade the MSnbase version from 2.4.0 to 2.8.2 (see MSnbase News_). Almost all the new features may not concern our usage of MSnbase. - -**Version 2.4.0.0 - 29/03/2018** - -- NEW: a new dedicated tool to read the raw data. This function was previously included in xcms.findChromPeaks. This way, you will now be able to display TICs and BPCs before xcms.findChromPeaks. |
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| diff -r 11ab2081bd4a -r 7faf9b2d83f6 lib.r --- a/lib.r Mon Apr 12 09:35:02 2021 +0000 +++ b/lib.r Mon Sep 11 09:24:51 2023 +0000 |
| [ |
| b'@@ -4,12 +4,12 @@\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+ 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@@ -17,237 +17,247 @@\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- cat("Main packages:\\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)) {\n- cat(paste(pkg, packageVersion(pkg)), "\\t")\n- }\n- cat("\\n")\n+ sessioninfo <- sessionInfo()\n+ cat(sessioninfo$R.version$version.string, "\\n")\n+ cat("Main packages:\\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)) {\n+ cat(paste(pkg, packageVersion(pkg)), "\\t")\n+ }\n+ 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+ 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- md5sumList <- NULL\n- for (image in args$images) {\n+ chromTIC <- NULL\n+ chromBPI <- NULL\n+ chromTIC_adjusted <- NULL\n+ chromBPI_adjusted <- NULL\n+ md5sumList <- NULL\n+ for (image in args$images) {\n \n- load(image)\n- # Handle infiles\n- if (!exists("singlefile")) singlefile <- NULL\n- if (!exists("zipfile")) zipfile <- NULL\n- rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)\n- zipfile <- rawFilePath$zipfile\n- singlefile <- rawFilePath$singlefile\n+ load(image)\n+ # Handle infiles\n+ if (!exists("singlefile")) singlefile <- NULL\n+ if (!exists("zipfile")) zipfile <- NULL\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+ 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- singlefile_merged <- singlefile\n- md5sumList_merged <- md5sumList\n- sampleNamesList_merged <- sampleNamesList\n- chromTIC_merged <- chromTIC\n- chromBPI_merged <- c'..b'e_galaxyPath, singlefile_sampleName)\n- files <- c(files, singlefile_sampleName)\n- }\n+ if (!suppressWarnings(try(file.link(singlefile_galaxyPath, singlefile_sampleName), silent = TRUE)))\n+ file.copy(singlefile_galaxyPath, singlefile_sampleName)\n+ files <- c(files, singlefile_sampleName)\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- print(error_message)\n- stop(error_message)\n- }\n- suppressWarnings(unzip(zipfile, unzip = "unzip"))\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+ print(error_message)\n+ stop(error_message)\n+ }\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+ #get the directory name\n+ suppressWarnings(filesInZip <- unzip(zipfile, list = TRUE))\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, "$", sep = ""), collapse = "|")\n- info <- file.info(directory)\n- listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)\n- files <- c(directory[!info$isdir], listed)\n- exists <- file.exists(files)\n- files <- files[exists]\n+ filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")\n+ filepattern <- paste(paste("\\\\.", filepattern, "$", sep = ""), collapse = "|")\n+ info <- file.info(directory)\n+ listed <- list.files(directory[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)\n+ files <- c(directory[!info$isdir], listed)\n+ exists <- file.exists(files)\n+ files <- files[exists]\n \n- }\n- return(list(zipfile = zipfile, singlefile = singlefile, files = files))\n-\n+ }\n+ return(list(zipfile = zipfile, singlefile = singlefile, files = files))\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+ # 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 11ab2081bd4a -r 7faf9b2d83f6 macros_xcms.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_xcms.xml Mon Sep 11 09:24:51 2023 +0000 |
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| b'@@ -0,0 +1,277 @@\n+<?xml version="1.0"?>\n+<macros>\n+\n+ <token name="@TOOL_VERSION@">3.12.0</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n+ <token name="@PROFILE@">21.09</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>\n+ <requirement type="package" version="1.1_5">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.element_identifier ) 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,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: 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_file" token_filename="">\n+ <section name="file_load_section">\n+ <conditional name="file_load_conditional">\n+ <param name="file_load_select"'..b'pe="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+.. _news: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS\n+\n+ </token>\n+\n+ <token name="@HELP_XCMS_NEWVERSION_3440@">\n+**Version 3.4.4.0 - 08/02/2019**\n+\n+- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS news_)\n+ </token>\n+ <token name="@HELP_XCMS_NEWVERSION_3610@">\n+**Version 3.6.1+galaxy* - 03/09/2019**\n+\n+- UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS news_)\n+ </token>\n+ <token name="@HELP_XCMS_NEWVERSION_31200@">\n+**Version 3.12.0+galaxy* - 03/03/2020**\n+\n+- UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS news_)\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 11ab2081bd4a -r 7faf9b2d83f6 msnbase_readmsdata.r --- a/msnbase_readmsdata.r Mon Apr 12 09:35:02 2021 +0000 +++ b/msnbase_readmsdata.r Mon Sep 11 09:24:51 2023 +0000 |
| [ |
| @@ -11,19 +11,21 @@ #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 = "/")) + 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") loadAndDisplayPackages(pkgs) -cat("\n\n"); +cat("\n\n") # ----- 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 = FALSE, quote = FALSE, sep = "\t") cat("\n\n") |
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| diff -r 11ab2081bd4a -r 7faf9b2d83f6 msnbase_readmsdata.xml --- a/msnbase_readmsdata.xml Mon Apr 12 09:35:02 2021 +0000 +++ b/msnbase_readmsdata.xml Mon Sep 11 09:24:51 2023 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@+galaxy0"> +<tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@+galaxy1"> <description>Imports mass-spectrometry data files</description> <macros> @@ -17,7 +17,7 @@ #set $source = $os.readlink(str($input)) singlefile_galaxyPath '$source' singlefile_sampleName '$os.path.basename($source)' #else - singlefile_galaxyPath '$input' singlefile_sampleName '$input.name' + singlefile_galaxyPath '$input' singlefile_sampleName '$input.element_identifier' #end if #else zipfile '$input' @@ -28,7 +28,7 @@ <inputs> - <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the following formats: mzxml, mzml, mzdata and netcdf. Zip file mode for the following formats: no_unzip.zip, zip. See the help section below." /> + <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the following formats: mzxml, mzml, mzdata and netcdf. Zip file mode for the following formats: zip. See the help section below." /> </inputs> @@ -41,7 +41,7 @@ <tests> - <test> + <test expect_num_outputs="2"> <param name="input" value="faahKO_reduce.zip" ftype="zip" /> <assert_stdout> <has_text text="rowNames: faahKO_reduce/KO/ko15.CDF faahKO_reduce/KO/ko16.CDF" /> @@ -55,7 +55,7 @@ </assert_stdout> <output name="sampleMetadata" value="sampleMetadata.tsv" /> </test> - <test> + <test expect_num_outputs="1"> <param name="input" value="ko15.CDF" ftype="netcdf" /> <assert_stdout> <has_text text="rowNames: ko15.CDF" /> @@ -123,7 +123,7 @@ ========================= ========================================== Name Format ========================= ========================================== -Upload File mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip +Upload File mzxml,mzml,mzdata,netcdf,zip ========================= ========================================== The easier way to process is to create a Dataset Collection of the type List @@ -185,14 +185,6 @@ **Step 3 : Uploading it to our Galaxy server** -If your zip file is less than 2Gb, you can use the Get Data tool to upload it. - -Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO_ on workflow4metabolomics.org. - -.. _HOWTO: http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf - -For more information, do not hesitate to send us an email at supportATworkflow4metabolomics.org. - Advices for converting your files into mzXML format (XCMS input) ---------------------------------------------------------------- |
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| diff -r 11ab2081bd4a -r 7faf9b2d83f6 repository_dependencies.xml --- a/repository_dependencies.xml Mon Apr 12 09:35:02 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -<?xml version="1.0" ?> -<repositories> - <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 |
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| diff -r 11ab2081bd4a -r 7faf9b2d83f6 static/images/xcms_fillpeaks_workflow.png |
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| @@ -0,0 +1,165 @@ +<!DOCTYPE html> +<HTML lang='en'> +<HEAD> +<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' /> +<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; } +th { background: #898989; text-align:left;color: white;} +h2 { color: #FFA212; } +ul li { margin-bottom:10px; } +</style> +</HEAD> +<BODY> +<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1> +By: planemo@galaxyproject.org - +Date: 230525-08:53:25 +</div> +<h2>Samples used:</h2> +<div><table> +<tr><th>sample</th><th>filename</th></tr> +<tr><td>ko15</td><td>ko15.CDF</td></tr><tr><td>ko16</td><td>ko16.CDF</td></tr><tr><td>wt15</td><td>wt15.CDF</td></tr><tr><td>wt16</td><td>wt16.CDF</td></tr> +</table> + +</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>Mon May 11 09:37:30 2020</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 May 11 09:37:49 2020</td><td>Peak grouping</td><td colspan='2'><pre> +Object of class: PeakDensityParam +Parameters: + sampleGroups: character of length 4 + bw: 5 + minFraction: 0.3 + minSamples: 1 + binSize: 0.01 + maxFeatures: 50 +</pre></td></tr> +<tr><td>Mon May 11 09:38:08 2020</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 + subset: + number of peak groups: 53 +</pre></td></tr> +<tr><td>Mon May 11 09:38:09 2020</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>Mon May 11 09:38:18 2020</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: 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: 1.55 Mb +- - - Spectra data - - - + MS level(s): 1 + Number of spectra: 5112 + MSn retention times: 41:38 - 75:7 minutes +- - - Processing information - - - +Data loaded [Mon May 11 09:37:30 2020] + MSnbase version: 2.10.1 +- - - Meta data - - - +phenoData + rowNames: 1 2 3 4 + 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 (31 total) + fvarMetadata: labelDescription +experimentData: use 'experimentData(object)' +- - - xcms preprocessing - - - +Chromatographic peak detection: + method: centWave + 15405 peaks identified in 4 samples. + On average 3851 chromatographic peaks per sample. +Alignment/retention time adjustment: + method: peak groups +Correspondence: + method: chromatographic peak density + 6349 features identified. + Median mz range of features: 0 + Median rt range of features: 0 + 6154 filled peaks (on average 1538.5 per sample). +</pre></div> +<h2>Informations about the xcmsSet object:</h2> +<div><pre> +An "xcmsSet" object with 4 samples + +Time range: 2509.2-4481.8 seconds (41.8-74.7 minutes) +Mass range: 200.1-600 m/z +Peaks: 15405 (about 3851 per sample) +Peak Groups: 6349 +Sample classes: KO, WT + +Feature detection: + o Peak picking performed on MS1. + o Scan range limited to 1 - 1278 +Profile settings: method = bin + step = 0.1 + +Memory usage: 3.98 MB +</pre></div> +<h2>Citations:</h2> +<div><ul> +<li>To cite the <b>XCMS</b> package in publications use: +<ul> +<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> +<li>Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)</li> +<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> +</ul> +</li> +<li>To cite the <b>CAMERA</b> package in publications use: +<ul> +<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> +</ul> +</li> +<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use: +<ul> +<li>Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813</li> +</ul> +</li> +</ul></div> +</BODY> +</HTML> |
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|
| b |
| diff -r 11ab2081bd4a -r 7faf9b2d83f6 test-data/faahKO.xset.group.variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO.xset.group.variableMetadata.tsv Mon Sep 11 09:24:51 2023 +0000 |
| b |
| b'@@ -0,0 +1,8373 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| diff -r 11ab2081bd4a -r 7faf9b2d83f6 test-data/noclass.merged.sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/noclass.merged.sampleMetadata.tsv Mon Sep 11 09:24:51 2023 +0000 |
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| @@ -0,0 +1,5 @@ +sample_name class +ko15 . +ko16 . +wt15 . +wt16 . |
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| diff -r 11ab2081bd4a -r 7faf9b2d83f6 test-data/roiList.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/roiList.txt Mon Sep 11 09:24:51 2023 +0000 |
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| diff -r 11ab2081bd4a -r 7faf9b2d83f6 test-data/sampleMetadata.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampleMetadata.tab Mon Sep 11 09:24:51 2023 +0000 |
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