| Previous changeset 27:d45a786cbc40 (2021-04-07) Next changeset 29:71572faf938e (2024-07-15) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e |
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modified:
abims_xcms_group.xml lib.r macros_xcms.xml xcms_group.r |
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added:
static/images/msnbase_readmsdata_workflow.png static/images/xcms_fillpeaks_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/MM14.mzML 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.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_reduce.zip test-data/ko15-raw.RData test-data/ko15-xset.RData test-data/ko16-raw.RData test-data/ko16-xset.RData test-data/noclass.merged.sampleMetadata.tsv test-data/roiList.txt test-data/sampleMetadata.tab test-data/sampleMetadata.tsv test-data/sampleMetadata_missing.tab test-data/wt15-raw.RData test-data/wt15-xset.RData test-data/wt16-raw.RData test-data/wt16-xset.RData |
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removed:
README.rst repository_dependencies.xml |
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| diff -r d45a786cbc40 -r 2b676d5eb848 README.rst --- a/README.rst Wed Apr 07 12:06:33 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,73 +0,0 @@ - -Changelog/News --------------- - -.. _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 3.6.1.0 - 03/09/2019** - -- UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_) - -**Version 3.4.4.0 - 08/02/2019** - -- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) - -- BUGFIX: issue with Inf values in the exported DataMatrix: https://github.com/sneumann/xcms/issues/323#issuecomment-433044378 - -**Version 3.0.0.1 - 09/11/2018** - -- BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist - -**Version 3.0.0.0 - 08/03/2018** - -- UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed. - -- NEW: a bunch of new options: PeakDensity.minSamples), MzClust.minSamples) - -- NEW: a new density plot - -- IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values. - - -**Version 2.1.1 - 29/11/2017** - -- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C - - -**Version 2.1.0 - 07/02/2017** - -- IMPROVEMENT: Add an option to export the peak list at this step without have to wait camara.annotate - -- IMPROVEMENT: xcms.group can deal with merged individual data from "xcms.xcmsSet Merger" - -- BUGFIX: the default value of "density" -> "Maximum number of groups to identify in a single m/z slice" which was of 5 have been changed to fix with the XMCS default values to 50 - - -**Version 2.0.6 - 06/07/2016** - -- UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 - - -**Version 2.0.5 - 04/04/2016** - -- TEST: refactoring to pass planemo test using conda dependencies - - -**Version 2.0.4 - 10/02/2016** - -- BUGFIX: better management of errors. Datasets remained green although the process failed - -- UPDATE: refactoring of internal management of inputs/outputs - -- UPDATE: refactoring to feed the new report tool - - -**Version 2.0.2 - 02/06/2015** - -- IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors. - -- IMPROVEMENT: parameter labels have changed to facilitate their reading. |
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| diff -r d45a786cbc40 -r 2b676d5eb848 abims_xcms_group.xml --- a/abims_xcms_group.xml Wed Apr 07 12:06:33 2021 +0000 +++ b/abims_xcms_group.xml Mon Sep 11 09:16:31 2023 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@TOOL_VERSION@+galaxy0"> +<tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Perform the correspondence, the grouping of chromatographic peaks within and between samples.</description> @@ -203,7 +203,7 @@ </test> --> <!-- from retcor --> - <test> + <test expect_num_outputs="4"> <param name="image" value="faahKO-single-class.xset.merged.group.retcor.RData" ftype="rdata"/> <conditional name="methods"> <param name="method" value="PeakDensity"/> |
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| diff -r d45a786cbc40 -r 2b676d5eb848 lib.r --- a/lib.r Wed Apr 07 12:06:33 2021 +0000 +++ b/lib.r Mon Sep 11 09:16:31 2023 +0000 |
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| 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 d45a786cbc40 -r 2b676d5eb848 macros_xcms.xml --- a/macros_xcms.xml Wed Apr 07 12:06:33 2021 +0000 +++ b/macros_xcms.xml Mon Sep 11 09:16:31 2023 +0000 |
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| @@ -2,6 +2,8 @@ <macros> <token name="@TOOL_VERSION@">3.12.0</token> + <token name="@VERSION_SUFFIX@">1</token> + <token name="@PROFILE@">21.09</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement> @@ -17,7 +19,7 @@ #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 ] ) + #set singlefile_sampleName = '|'.join( [ str( $single_file.element_identifier ) for $single_file in $file_load_section.file_load_conditional.input ] ) singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' #else @@ -36,7 +38,7 @@ <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." /> + <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." /> </when> </conditional> </section> @@ -80,7 +82,7 @@ <!-- PEAKLIST --> <token name="@COMMAND_PEAKLIST@"> - #if $peaklist.peaklistBool + #if $peaklist.peaklistBool == 'true' convertRTMinute $peaklist.convertRTMinute numDigitsMZ $peaklist.numDigitsMZ numDigitsRT $peaklist.numDigitsRT @@ -103,14 +105,17 @@ <xml name="input_peaklist_section"> <section name="peaklist" title="Peak List" expanded="True"> - <param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" /> + <param name="peaklistBool" type="hidden" label="Get the Peak List" value="true" /> <expand macro="input_peaklist"/> </section> </xml> <xml name="input_peaklist_conditional"> <conditional name="peaklist"> - <param name="peaklistBool" type="boolean" label="Get the Peak List" /> + <param name="peaklistBool" type="select" label="Get the Peak List"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> <when value="true"> <expand macro="input_peaklist"/> </when> @@ -120,10 +125,10 @@ <xml name="output_peaklist" token_function=""> <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" > - <filter>(peaklist['peaklistBool'])</filter> + <filter>peaklist['peaklistBool'] == 'true'</filter> </data> <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" > - <filter>(peaklist['peaklistBool'])</filter> + <filter>peaklist['peaklistBool'] == 'true'</filter> </data> </xml> @@ -243,24 +248,24 @@ .. _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 +.. _news: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS </token> <token name="@HELP_XCMS_NEWVERSION_3440@"> **Version 3.4.4.0 - 08/02/2019** -- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) +- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS news_) </token> <token name="@HELP_XCMS_NEWVERSION_3610@"> **Version 3.6.1+galaxy* - 03/09/2019** -- UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_) +- 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_) +- UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS news_) </token> <xml name="citation"> |
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| diff -r d45a786cbc40 -r 2b676d5eb848 repository_dependencies.xml --- a/repository_dependencies.xml Wed Apr 07 12:06:33 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 d45a786cbc40 -r 2b676d5eb848 test-data/MM14.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MM14.mzML Mon Sep 11 09:16:31 2023 +0000 |
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| b'@@ -0,0 +1,3667 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" accession="" version="1.1">\n+\t<cvList count="2">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+\t\t<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n+\t\t</fileContent>\n+\t\t<sourceFileList count="1">\n+\t\t\t<sourceFile id="sf_ru_0" name="analysis.baf" location="MM14_20uM_2-A%2c4_01_1745.d/">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="" 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| diff -r d45a786cbc40 -r 2b676d5eb848 test-data/TICs.pdf |
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| Binary file test-data/TICs.pdf has changed |
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| diff -r d45a786cbc40 -r 2b676d5eb848 test-data/faahKO-single-class.xset.group.retcor.group.fillPeaks.dataMatrix.NAless.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO-single-class.xset.group.retcor.group.fillPeaks.dataMatrix.NAless.tsv Mon Sep 11 09:16:31 2023 +0000 |
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|
| b |
| diff -r d45a786cbc40 -r 2b676d5eb848 test-data/faahKO-single-class.xset.group.retcor.group.fillPeaks.variableMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO-single-class.xset.group.retcor.group.fillPeaks.variableMetadata.tsv Mon Sep 11 09:16:31 2023 +0000 |
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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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| diff -r d45a786cbc40 -r 2b676d5eb848 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 09:16:31 2023 +0000 |
| b |
| @@ -0,0 +1,5 @@ +sample_name class +ko15 . +ko16 . +wt15 . +wt16 . |
| b |
| diff -r d45a786cbc40 -r 2b676d5eb848 test-data/roiList.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/roiList.txt Mon Sep 11 09:16:31 2023 +0000 |
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| @@ -0,0 +1,2 @@ +scmin scmax mzmin mzmax length intensity +200 300 300 350 100 5000 |
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| diff -r d45a786cbc40 -r 2b676d5eb848 test-data/sampleMetadata.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampleMetadata.tab Mon Sep 11 09:16:31 2023 +0000 |
| b |
| @@ -0,0 +1,6 @@ +wt16 WT +ko16 KO +wt15 WT +ko15 KO +ko10 KO +foobar01 FOOBAR |
| b |
| diff -r d45a786cbc40 -r 2b676d5eb848 test-data/sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampleMetadata.tsv Mon Sep 11 09:16:31 2023 +0000 |
| b |
| @@ -0,0 +1,5 @@ +sample_name class +ko15 KO +ko16 KO +wt15 WT +wt16 WT |
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| diff -r d45a786cbc40 -r 2b676d5eb848 test-data/sampleMetadata_missing.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampleMetadata_missing.tab Mon Sep 11 09:16:31 2023 +0000 |
| b |
| @@ -0,0 +1,5 @@ +wt16 WT +wt15 WT +ko15 KO +ko10 KO +foobar01 FOOBAR |
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| diff -r d45a786cbc40 -r 2b676d5eb848 test-data/wt15-raw.RData |
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| Binary file test-data/wt15-raw.RData has changed |
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| diff -r d45a786cbc40 -r 2b676d5eb848 test-data/wt15-xset.RData |
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| Binary file test-data/wt15-xset.RData has changed |
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| diff -r d45a786cbc40 -r 2b676d5eb848 test-data/wt16-raw.RData |
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| Binary file test-data/wt16-raw.RData has changed |
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| diff -r d45a786cbc40 -r 2b676d5eb848 test-data/wt16-xset.RData |
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| Binary file test-data/wt16-xset.RData has changed |
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| diff -r d45a786cbc40 -r 2b676d5eb848 xcms_group.r --- a/xcms_group.r Wed Apr 07 12:06:33 2021 +0000 +++ b/xcms_group.r Mon Sep 11 09:16:31 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("xcms", "batch", "RColorBrewer") 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") @@ -81,7 +83,7 @@ getPlotChromPeakDensity(xdata, param = groupChromPeaksParam) if (exists("intval")) { - getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv") + getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv") } cat("\n\n") |
