| Previous changeset 9:94eb263cfab4 (2021-04-07) Next changeset 11:4ea32e46b2d6 (2024-07-15) |
|
Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e |
|
modified:
lib.r macros_xcms.xml xcms_export_samplemetadata.r xcms_export_samplemetadata.xml |
|
added:
static/images/msnbase_readmsdata_workflow.png static/images/xcms_fillpeaks_workflow.png static/images/xcms_group.png static/images/xcms_group_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.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/faahKO_reduce.zip test-data/ko15-raw.RData test-data/ko15.CDF test-data/ko16-raw.RData test-data/ko16.CDF 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.CDF test-data/wt16-raw.RData test-data/wt16.CDF |
|
removed:
README.rst repository_dependencies.xml |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 README.rst --- a/README.rst Wed Apr 07 09:53:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,34 +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 3.4.3.0 - 08/02/2019** - -- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.3 - -**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 underlining codes and methods - -- IMPROVMENT: a new dedicated tool "xcms plot chromatogram" will allow you to get TIC and BPI of your raw data. - -- IMPROVMENT: the tool will now generate a sampleMetadata file if any was provided. It will be useful to add some further information for the normalization and statistics steps. - -**Version 1.0.1 - 13/02/2017** - -- IMPROVMENT: the tool will now raise an error if a sample isn't describe in the sampleMetadata file - - -**Version 1.0.0 - 03/02/2017** - -- NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 lib.r --- a/lib.r Wed Apr 07 09:53:54 2021 +0000 +++ b/lib.r Mon Sep 11 09:14:35 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' |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 macros_xcms.xml --- a/macros_xcms.xml Wed Apr 07 09:53:54 2021 +0000 +++ b/macros_xcms.xml Mon Sep 11 09:14:35 2023 +0000 |
| [ |
| @@ -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"> |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 repository_dependencies.xml --- a/repository_dependencies.xml Wed Apr 07 09:53:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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 |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 static/images/msnbase_readmsdata_workflow.png |
| b |
| Binary file static/images/msnbase_readmsdata_workflow.png has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 static/images/xcms_fillpeaks_workflow.png |
| b |
| Binary file static/images/xcms_fillpeaks_workflow.png has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 static/images/xcms_group.png |
| b |
| Binary file static/images/xcms_group.png has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 static/images/xcms_group_workflow.png |
| b |
| Binary file static/images/xcms_group_workflow.png has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 static/images/xcms_plot_chromatogram_workflow.png |
| b |
| Binary file static/images/xcms_plot_chromatogram_workflow.png has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 static/images/xcms_retcor.png |
| b |
| Binary file static/images/xcms_retcor.png has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 static/images/xcms_retcor_workflow.png |
| b |
| Binary file static/images/xcms_retcor_workflow.png has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 static/images/xcms_summary_workflow.png |
| b |
| Binary file static/images/xcms_summary_workflow.png has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 static/images/xcms_tics.png |
| b |
| Binary file static/images/xcms_tics.png has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 static/images/xcms_xcmsset_workflow.png |
| b |
| Binary file static/images/xcms_xcmsset_workflow.png has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/BPIs.pdf |
| b |
| Binary file test-data/BPIs.pdf has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/MM14.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MM14.mzML Mon Sep 11 09:14:35 2023 +0000 |
| b |
| 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="" />\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000564" name="PSI mzData file" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000824" name="no nativeID format" />\n+\t\t\t</sourceFile>\n+\t\t</sourceFileList>\n+\t\t<contact>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Customer, Bruker" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value="" />\n+\t\t</contact>\n+\t</fileDescription>\n+\t<sampleList count="1">\n+\t\t<sample id="sa_0" name="MM14_20uM">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="3">\n+\t\t<software id="so_in_0" version="" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t\t<software id="so_dp_0" version="1.3.3" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000717" name="CompassXport" />\n+\t\t</software>\n+\t\t<software id="so_dp_1" version="1.4" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000756" name="FileConverter" />\n+\t\t</software>\n+\t</softwareList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="ic_0">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />\n+\t\t\t<componentList count="3">\n+\t\t\t\t<source order="0">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" />\n+\t\t\t\t</source>\n+\t\t\t\t<analyzer order="0">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unitName="meter" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="0" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000443" name="mass analyzer type" />\n+\t\t\t\t</analyzer>\n+\t\t\t\t<detector order="0">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="0" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="0" unitAccession="UO:0000106" unitName="hertz" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000026" name="detector type" />\n+\t\t\t\t</detector>\n+\t\t\t</componentList>\n+\t\t\t<softwareRef ref="so_in_0" />\n+\t\t</instrumentConfiguration>\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n+\t\t<dataProcessing id="dp_ru_0">\n+\t\t\t<processingMethod order="0" softwareRef="so_dp_0">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000034" name="charge deconvolution" />\n+\t\t\t\t<cvP'..b'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</binary>\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n\\ No newline at end of file\n' |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/TICs.pdf |
| b |
| Binary file test-data/TICs.pdf has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 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 09:14:35 2023 +0000 |
| b |
| b'@@ -0,0 +1,8210 @@\n+name\tko15\tko16\twt15\twt16\n+M200T2874\t81222.2440209194\t506848.884266667\t54341.7228406609\t72996.8772876537\n+M200T3531\t0\t0\t4586.52650000006\t0\n+M200T3486\t6029.94499999992\t0\t0\t0\n+M200T3675\t0\t0\t5108.15999999988\t2578.12031346051\n+M200T3190\t0\t4333.4849999999\t0\t0\n+M200T3875\t1144.01499999999\t553.365929229532\t585.097402094442\t0\n+M200T3810\t0\t0\t1018.81499999998\t0\n+M200T3971\t1326.99047756647\t0\t0\t1242.61000000004\n+M201T3543\t0\t2863.6449999999\t0\t0\n+M201T3778\t1306.08395530754\t0\t1680.81000000006\t0\n+M201T4059\t0\t0\t1339.64000000005\t275.481792795915\n+M201T3626\t0\t1413.45327423963\t854.929689324458\t2931.24499999993\n+M201T2556\t0\t14307.2299999999\t0\t0\n+M201T3275\t0\t911.509653323359\t4090.91000000014\t1614.20733427184\n+M201T3144\t26391.7866084706\t254581.758476187\t67292.0303792526\t26660.982146465\n+M201T3509\t4023.61499999999\t809.701273510851\t0\t0\n+M201T3993\t0\t0\t1657.33500000006\t0\n+M201T3685\t0\t1357.29564957504\t2906.20499999993\t0\n+M201T4062\t452.373331200482\t154.812206677498\t1275.47500000004\t0\n+M201T3793\t0\t1095.56869762467\t764.395031558866\t3245.80999999992\n+M201T4153\t0\t774.575999999962\t0\t0\n+M201T3880\t0\t1220.70000000004\t543.598893098522\t0\n+M201T4031\t0\t0\t0\t1220.69999999998\n+M201T3931\t224.441862853321\t0\t1284.72816666668\t0\n+M202T3853\t892.050000000031\t0\t0\t0\n+M202T4016\t0\t0\t831.015000000029\t0\n+M202T3304\t2759.095\t0\t222.491774086216\t760.611413736599\n+M202T4066\t460.333530121371\t0\t754.233600000007\t0\n+M202T3323\t3588.54500000001\t0\t2559.66082485416\t0\n+M202T3175\t7682.58500000004\t0\t0\t0\n+M202T3279\t0\t3872.96250000005\t0\t0\n+M202T3377\t9879.84499999977\t0\t0\t0\n+M202T3758\t0\t615.397896487242\t1151.71733333335\t0\n+M202T3191\t13286.7187522747\t3806.07999999999\t1995.18577676705\t3419.83041531475\n+M202T3893\t307.128739960908\t841.96999999998\t0\t1486.73784949229\n+M202T4031\t0\t688.600000000024\t0\t0\n+M202T4007\t1275.90358353372\t1629.165\t855.896594763284\t142.943555001703\n+M202T3273\t77227.3769090911\t6336.46132607919\t41368.5521695297\t8552.81534614336\n+M202T4136\t0\t0\t0\t732.419999999983\n+M202T3937\t171.88228228494\t0\t1461.71\t153.596933105691\n+M202T2900\t36435.3079999996\t5525.63941512457\t19864.739322544\t6451.89183150446\n+M202T3290\t0\t0\t0\t3372.57500000002\n+M203T4032\t0\t0\t0\t978.124999999977\n+M203T3316\t0\t0\t0\t1136.19000000004\n+M203T3303\t1201.83163242771\t1694.89499999996\t0\t2159.29083292845\n+M203T3974\t890.31885881458\t0\t2796.65500000002\t3072.1139554695\n+M203T3348\t0\t2974.74816666671\t0\t0\n+M203T4139\t0\t1020.37999999998\t154.767063018545\t873.748229193302\n+M203T2682\t0\t0\t0\t6346.07499999991\n+M203T4177\t285.337655328169\t804.409999999981\t0\t843.833919720499\n+M203T3790\t0\t2690.23500000009\t0\t426.450339756003\n+M203T3718\t1765.04806212748\t0\t0\t3345.96999999992\n+M203T3328\t3852.53759999981\t0\t0\t0\n+M203T4051\t0\t0\t1647.82847523149\t1550.91499999999\n+M204T3525\t0\t134.343793394769\t967.169999999987\t0\n+M204T4123\t0\t235.773587961221\t0\t793.455000000074\n+M204T3060\t3905.96266666662\t0\t0\t403.436877641033\n+M204T4020\t1111.14999999999\t1701.07494147464\t0\t129.14885672801\n+M204T3664\t3002.85120000003\t0\t390.754388277302\t0\n+M204T4138\t0\t0\t0\t1089.24000000004\n+M204T3837\t0\t1931.69724296033\t1676.11500000006\t1954.33432002628\n+M204T2629\t0\t0\t3518.12000000012\t0\n+M204T3395\t1253.10430764421\t180.736198217915\t1132.61350883226\t1586.91\n+M204T4073\t0\t1062.63500000004\t0\t0\n+M204T3700\t0\t0\t0\t1446.05999999997\n+M204T3598\t498.492104159176\t0\t0\t1032.90000000004\n+M205T3576\t2130.23679473948\t0\t0\t2466.43999999994\n+M205T2588\t2646.10199999996\t0\t0\t9189.67999999988\n+M205T2788\t1924712.01585714\t1757150.9648\t2129885.09357143\t1634341.9855862\n+M205T4038\t2600.69759999987\t0\t0\t0\n+M205T3779\t2777.8750000001\t0\t5180.14999999997\t0\n+M205T3756\t0\t0\t2425.44000000002\t0\n+M205T3915\t0\t3392.55866666671\t0\t558.088024839385\n+M205T4061\t0\t0\t1198.79000000004\t0\n+M206T4077\t0\t737.513206260254\t793.454999999982\t0\n+M206T3350\t289.453782284636\t0\t641.649999999985\t0\n+M206T3091\t0\t0\t0\t4682.47999999989\n+M206T3290\t0\t0\t0\t1023.50999999998\n+M206T3197\t2227.66841463593\t10174.0649999999\t0\t0\n+M206T4102\t1685.41525000004\t1285.76008820482\t956.564140688575\t441.225982011306\n+M206T2789\t213659.293920001\t215348.980072334\t253825.557279999\t241844'..b'\t0\t0\t3350.66499999992\t0\n+M598T3059\t1296.99898550837\t0\t3904.17600000003\t0\n+M598T2567\t1277.03999999998\t845.099999999989\t5259.96499999993\t503.303999999993\n+M598T3682\t0\t0\t0\t2907.39840000003\n+M598T3251\t0\t0\t11160.015\t0\n+M598T3574\t4893.75500000017\t0\t0\t0\n+M598T3162\t0\t1611.83839245526\t0\t1547.78500000005\n+M598T3739\t6735.75999999984\t1846.14789644079\t0\t0\n+M598T2989\t0\t7907.94500000028\t0\t0\n+M598T3712\t6340.95496921884\t0\t8317.50789686137\t48876.8056363635\n+M598T3726\t5065.11907009344\t29323.4050000004\t1188.54774219024\t5153.7168624086\n+M598T3846\t0\t19344.1924374998\t2843.47898603692\t17477.561927071\n+M598T4219\t0\t0\t0\t852.92499999998\n+M598T3695\t23734.0885778205\t0\t5562.67701042668\t28572.205000001\n+M598T3810\t10930.0351206905\t201593.909999999\t2211.73261497696\t52820.9858652353\n+M598T3222\t0\t16185.5021250003\t7981.85791479311\t9672.11419392324\n+M598T2834\t5337.7886250001\t4769.77488860455\t0\t1082.8565562429\n+M598T3494\t0\t0\t9308.62000000032\t0\n+M598T3406\t3215.24900439939\t2824.98156517161\t4532.24000000016\t0\n+M598T3701\t15814.7232228657\t284728.444599503\t17560.9153406495\t65022.6200000009\n+M598T4231\t1558.64039999994\t0\t481.721707478611\t753.016243098335\n+M598T3366\t6077.15236111283\t0\t0\t7501.04499999995\n+M598T3118\t3137.82499999993\t0\t0\t0\n+M598T3821\t974.843575102324\t126881.278714286\t4933.04464297469\t2509.38182349615\n+M598T2674\t2139.08160000002\t2826.02880000002\t0\t0\n+M598T3182\t0\t2838.6076666667\t0\t0\n+M598T2531\t0\t1600.99499999996\t0\t0\n+M598T4017\t4444.59999999997\t0\t0\t0\n+M598T2953\t5756.0700000002\t1724.33725246677\t0\t0\n+M598T2766\t0\t5078.42499999999\t0\t1126.16751586958\n+M599T4225\t0\t333.435154724117\t0\t881.094999999979\n+M599T3183\t0\t0\t0\t2164.39499999999\n+M599T2849\t0\t0\t0\t3757.56499999997\n+M599T2933\t0\t2557.20999999994\t0\t0\n+M599T2619\t0\t2237.94999999995\t0\t2020.87814908812\n+M599T3094\t0\t0\t0\t5745.1150000002\n+M599T2622\t24597.6221333335\t1877.26774215633\t2986.80133766049\t2913.84489801312\n+M599T4186\t172.777302353793\t0\t769.979999999982\t0\n+M599T4200\t1370.93999999996\t0\t435.893105891126\t127.703058366541\n+M599T2879\t8102.55153537841\t2034.25918064264\t4434.28146373806\t3269.28500000002\n+M599T3740\t0\t8220.94499999976\t0\t3178.02394895968\n+M599T4152\t3017.34834896235\t1485.14525722476\t2044.19233123712\t5823.36499999964\n+M599T4163\t2207.85303515129\t8068.71033333314\t8682.74092229391\t6358.68509581886\n+M599T4135\t3863.03619876788\t668.238094124805\t13849.6178571426\t2114.93912264242\n+M599T3699\t0\t0\t55051.9369090907\t0\n+M599T3976\t1644.52916525785\t15327.6100000005\t3624.2365036493\t0\n+M599T3839\t0\t0\t5238.05500000018\t9571.48260942048\n+M599T3721\t22852.13\t0\t0\t0\n+M599T3472\t2227.71333573436\t1331.44296624522\t4981.33738414416\t6298.5500000001\n+M599T4051\t798856.451441174\t43788.0280595446\t897286.005000001\t53765.0063852351\n+M599T3919\t31084.7641242534\t2266219.01826094\t30473.0678060207\t2271127.28014893\n+M599T3746\t2472129.73859259\t0\t1608909.17335824\t11119.5679924219\n+M599T3732\t1815500.66662321\t0\t1909653.70493332\t4870.16694819183\n+M599T4122\t191155.502071291\t616126.953938585\t98308.1768952928\t707685.939314288\n+M599T3435\t35592.8437333336\t1324.16025714739\t0\t8010.54495184683\n+M599T2843\t3082.63932640015\t5415.77280000005\t2712.45484268696\t1196.90751696058\n+M599T4123\t2548.12222709097\t354770.43852632\t15271.7977908302\t222487.861494631\n+M599T2972\t6779.23216231205\t8383.79278134077\t0\t12502.4521250001\n+M599T3811\t79625.6350000028\t14078.913713385\t14098.4189970001\t8322.90451856661\n+M599T3724\t98775.5508124921\t0\t797434.72246154\t0\n+M600T3006\t0\t5849.96999999986\t0\t0\n+M600T3606\t0\t0\t0\t5001.73999999997\n+M600T2729\t0\t0\t0\t1760.62499999996\n+M600T3411\t3353.79499999992\t0\t0\t0\n+M600T2526\t0\t0\t3209.81499999996\t0\n+M600T2559\t0\t2928.1150000001\t0\t0\n+M600T2607\t6022.12000000021\t771.816899999981\t0\t2331.63714285708\n+M600T2784\t0\t0\t0\t2608.74386666668\n+M600T3457\t4671.52499999989\t0\t0\t2479.56486480522\n+M600T3441\t0\t8782.77999999999\t0\t0\n+M600T2840\t0\t0\t0\t1987.33833333336\n+M600T2539\t0\t3639.80233333338\t0\t1631.80820000002\n+M600T3077\t1572.35085978039\t0\t0\t3430.04160000003\n+M600T3351\t2327.15500000008\t0\t0\t0\n+M600T2967\t9211.58999999991\t0\t0\t6283.44519770874\n+M600T3213\t7784.31000000027\t2558.37040150977\t0\t0\n' |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 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 09:14:35 2023 +0000 |
| b |
| b'@@ -0,0 +1,8210 @@\n+name\tnamecustom\tmz\tmzmin\tmzmax\trt\trtmin\trtmax\tnpeaks\tKO\tWT\tpeakidx\tms_level\n+M200T2874\tM200.1T2873.7\t200.100006103516\t200.100006103516\t200.100006103516\t2873.68391134257\t2873.68391134257\t2873.68391134257\t1\t1\t0\t2697,9252,14081,16457\t1\n+M200T3531\tM200.2T3531.3\t200.199996948242\t200.199996948242\t200.199996948242\t3531.31964551099\t3531.31964551099\t3531.31964551099\t1\t0\t1\t5859\t1\n+M200T3486\tM200.2T3486\t200.199996948242\t200.199996948242\t200.199996948242\t3486.00509624482\t3486.00509624482\t3486.00509624482\t1\t1\t0\t1089\t1\n+M200T3675\tM200.2T3674.6\t200.199996948242\t200.199996948242\t200.199996948242\t3674.63855476221\t3674.63855476221\t3674.63855476221\t1\t0\t1\t6014,16458\t1\n+M200T3190\tM200.2T3189.7\t200.199996948242\t200.199996948242\t200.199996948242\t3189.72990501207\t3189.72990501207\t3189.72990501207\t1\t1\t0\t3054\t1\n+M200T3875\tM200.2T3875\t200.199996948242\t200.199996948242\t200.199996948242\t3874.99077191002\t3874.99077191002\t3874.99077191002\t1\t1\t0\t1677,11797,14082\t1\n+M200T3810\tM200.3T3810.4\t200.300003051758\t200.300003051758\t200.300003051758\t3810.3863558399\t3810.3863558399\t3810.3863558399\t1\t0\t1\t6249\t1\n+M200T3971\tM200.3T3970.7\t200.300003051758\t200.300003051758\t200.300003051758\t3970.6689733866\t3970.6689733866\t3970.6689733866\t1\t0\t1\t8804,9253\t1\n+M201T3543\tM200.8T3543.1\t200.800003051758\t200.800003051758\t200.800003051758\t3543.09033908212\t3543.09033908212\t3543.09033908212\t1\t1\t0\t3594\t1\n+M201T3778\tM200.8T3777.8\t200.800003051758\t200.800003051758\t200.800003051758\t3777.75694502411\t3777.75694502411\t3777.75694502411\t1\t0\t1\t6185,9254\t1\n+M201T4059\tM200.8T4059.1\t200.800003051758\t200.800003051758\t200.800003051758\t4059.13192366566\t4059.13192366566\t4059.13192366566\t1\t0\t1\t6585,16459\t1\n+M201T3626\tM200.9T3626\t200.900009155273\t200.900009155273\t200.900009155273\t3625.97718521666\t3625.97718521666\t3625.97718521666\t1\t0\t1\t8310,11798,14083\t1\n+M201T2556\tM200.9T2556.2\t200.900009155273\t200.900009155273\t200.900009155273\t2556.15469110982\t2556.15469110982\t2556.15469110982\t1\t1\t0\t2311\t1\n+M201T3275\tM200.9T3275.4\t200.900009155273\t200.900009155273\t200.900009155273\t3275.40538674132\t3275.40538674132\t3275.40538674132\t1\t0\t1\t5484,11799,16460\t1\n+M201T3144\tM201.1T3144\t201.100006103516\t201.100006103516\t201.100006103516\t3144.01642646625\t3144.01642646625\t3144.01642646625\t1\t1\t0\t3007,9255,14084,16461\t1\n+M201T3509\tM201.2T3509.1\t201.199996948242\t201.199996948242\t201.199996948242\t3509.07934422904\t3509.07934422904\t3509.07934422904\t1\t1\t0\t1133,11800\t1\n+M201T3993\tM201.2T3993.2\t201.199996948242\t201.199996948242\t201.199996948242\t3993.17884722681\t3993.17884722681\t3993.17884722681\t1\t0\t1\t6528\t1\n+M201T3685\tM201.2T3685.1\t201.199996948242\t201.199996948242\t201.199996948242\t3685.0696482451\t3685.0696482451\t3685.0696482451\t1\t0\t1\t6034,11801\t1\n+M201T4062\tM201.2T4062.3\t201.199996948242\t201.199996948242\t201.199996948242\t4062.34903397399\t4062.34903397399\t4062.34903397399\t1\t0\t1\t6593,9256,11802\t1\n+M201T3793\tM201.2T3792.9\t201.199996948242\t201.199996948242\t201.199996948242\t3792.85151270471\t3792.85151270471\t3792.85151270471\t1\t0\t1\t8577,11803,14085\t1\n+M201T4153\tM201.3T4153.2\t201.300003051758\t201.300003051758\t201.300003051758\t4153.15719367524\t4153.15719367524\t4153.15719367524\t1\t1\t0\t4557\t1\n+M201T3880\tM201.3T3880.4\t201.300003051758\t201.300003051758\t201.300003051758\t3880.38929268024\t3880.38929268024\t3880.38929268024\t1\t1\t0\t4093,14086\t1\n+M201T4031\tM201.3T4030.5\t201.300003051758\t201.300003051758\t201.300003051758\t4030.50506176065\t4030.50506176065\t4030.50506176065\t1\t0\t1\t8870\t1\n+M201T3931\tM201.3T3930.6\t201.300003051758\t201.300003051758\t201.300003051758\t3930.63678102149\t3930.63678102149\t3930.63678102149\t1\t0\t1\t6439,9257\t1\n+M202T3853\tM201.7T3853\t201.699996948242\t201.699996948242\t201.699996948242\t3853.02204433247\t3853.02204433247\t3853.02204433247\t1\t1\t0\t1623\t1\n+M202T4016\tM201.7T4015.7\t201.699996948242\t201.699996948242\t201.699996948242\t4015.69134696818\t4015.69134696818\t4015.69134696818\t1\t0\t1\t6548\t1\n+M202T3304\tM201.8T3303.6\t201.800003051758\t201.800003051758\t201.800003051758\t3303.62787160307\t3303.62787160307\t3303.62787160307\t1\t1\t0\t832,14087,1'..b'45221\t3975.94236545221\t1\t1\t0\t4253,11787,16449\t1\n+M599T3839\tM599.2T3838.6\t599.200012207031\t599.200012207031\t599.200012207031\t3838.59250927576\t3838.59250927576\t3838.59250927576\t1\t0\t1\t6302,18985\t1\n+M599T3721\tM599.2T3720.8\t599.200012207031\t599.200012207031\t599.200012207031\t3720.83203164455\t3720.83203164455\t3720.83203164455\t1\t1\t0\t1427\t1\n+M599T3472\tM599.2T3471.6\t599.200012207031\t599.200012207031\t599.200012207031\t3471.59423785259\t3471.59423785259\t3471.59423785259\t1\t0\t1\t8116,11788,14072,16450\t1\n+M599T4051\tM599.3T4051.1\t599.299987792969\t599.299987792969\t599.299987792969\t4051.08806403471\t4051.08806403471\t4056.49311245158\t3\t1\t1\t1980,6571,6597,14073,18986\t1\n+M599T3919\tM599.3T3918.8\t599.299987792969\t599.299987792969\t599.299987792969\t3918.84484914545\t3918.84484914545\t3918.84484914545\t2\t0\t1\t8717,8748,11789,14074,16451\t1\n+M599T3746\tM599.3T3745.5\t599.299987792969\t599.299987792969\t599.299987792969\t3745.52734731246\t3745.52734731246\t3745.52734731246\t1\t1\t0\t1481,16452,18987\t1\n+M599T3732\tM599.3T3731.7\t599.299987792969\t599.299987792969\t599.299987792969\t3731.74584176396\t3731.74584176396\t3731.74584176396\t1\t0\t1\t6133,11790,18988\t1\n+M599T4122\tM599.3T4121.8\t599.299987792969\t599.299987792969\t599.299987792969\t4121.82779290474\t4121.82779290474\t4121.82779290474\t1\t0\t1\t9058,11791,14075,16453\t1\n+M599T3435\tM599.3T3434.9\t599.299987792969\t599.299987792969\t599.299987792969\t3434.89281552429\t3434.89281552429\t3434.89281552429\t1\t1\t0\t1028,14076,18989\t1\n+M599T2843\tM599.4T2843.3\t599.400024414062\t599.400024414062\t599.400024414062\t2843.30486913571\t2843.30486913571\t2843.30486913571\t1\t1\t0\t2616,11792,16454,18990\t1\n+M599T4123\tM599.4T4123.4\t599.400024414062\t599.400024414062\t599.400024414062\t4123.37945202446\t4123.37945202446\t4123.37945202446\t1\t1\t0\t4466,11793,16455,18991\t1\n+M599T2972\tM599.4T2971.9\t599.400024414062\t599.400024414062\t599.400024414062\t2971.89456248078\t2971.89456248078\t2971.89456248078\t1\t0\t1\t7528,11794,14077\t1\n+M599T3811\tM599.4T3810.8\t599.400024414062\t599.400024414062\t599.400024414062\t3810.78838667034\t3810.78838667034\t3810.78838667034\t1\t1\t0\t1552,14078,16456,18992\t1\n+M599T3724\tM599.4T3724.2\t599.400024414062\t599.400024414062\t599.400024414062\t3724.15483079474\t3724.15483079474\t3724.15483079474\t1\t0\t1\t6112,11795\t1\n+M600T3006\tM599.5T3005.5\t599.5\t599.5\t599.5\t3005.5373832321\t3005.5373832321\t3005.5373832321\t1\t1\t0\t2885\t1\n+M600T3606\tM599.5T3606\t599.5\t599.5\t599.5\t3605.98210183342\t3605.98210183342\t3605.98210183342\t1\t0\t1\t8294\t1\n+M600T2729\tM599.5T2728.5\t599.5\t599.5\t599.5\t2728.54205746605\t2728.54205746605\t2728.54205746605\t1\t0\t1\t7235\t1\n+M600T3411\tM599.5T3411.1\t599.5\t599.5\t599.5\t3411.08772075784\t3411.08772075784\t3411.08772075784\t1\t1\t0\t999\t1\n+M600T2526\tM599.8T2526.4\t599.799987792969\t599.799987792969\t599.799987792969\t2526.41690686604\t2526.41690686604\t2526.41690686604\t1\t0\t1\t4673\t1\n+M600T2559\tM599.8T2559.3\t599.799987792969\t599.799987792969\t599.799987792969\t2559.28469110982\t2559.28469110982\t2559.28469110982\t1\t1\t0\t2316\t1\n+M600T2607\tM599.9T2606.6\t599.900024414062\t599.900024414062\t599.900024414062\t2606.59419045632\t2602.26343050377\t2610.92495040886\t2\t1\t1\t75,7054,14079\t1\n+M600T2784\tM599.9T2784\t599.900024414062\t599.900024414062\t599.900024414062\t2784.04015290081\t2784.04015290081\t2784.04015290081\t1\t0\t1\t7290\t1\n+M600T3457\tM600T3456.5\t600\t600\t600\t3456.54872252675\t3456.54872252675\t3456.54872252675\t1\t1\t0\t1049,18993\t1\n+M600T3441\tM600T3440.7\t600\t600\t600\t3440.71885541009\t3440.71885541009\t3440.71885541009\t1\t1\t0\t3394\t1\n+M600T2840\tM600T2840.2\t600\t600\t600\t2840.23577540144\t2840.23577540144\t2840.23577540144\t1\t0\t1\t7388\t1\n+M600T2539\tM600T2538.9\t600\t600\t600\t2538.94069110982\t2538.94069110982\t2538.94069110982\t1\t1\t0\t2295,18994\t1\n+M600T3077\tM600T3077\t600\t600\t600\t3077.01089094222\t3077.01089094222\t3077.01089094222\t1\t0\t1\t7609,11796\t1\n+M600T3351\tM600T3351\t600\t600\t600\t3351.00190207352\t3351.00190207352\t3351.00190207352\t1\t1\t0\t903\t1\n+M600T2967\tM600T2967\t600\t600\t600\t2967.02907897485\t2967.02907897485\t2967.02907897485\t1\t1\t0\t455,18995\t1\n+M600T3213\tM600T3213.3\t600\t600\t600\t3213.302355087\t3213.302355087\t3213.302355087\t1\t1\t0\t705,14080\t1\n' |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/faahKO-single-class.xset.merged.RData |
| b |
| Binary file test-data/faahKO-single-class.xset.merged.RData has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/faahKO-single-class.xset.merged.group.RData |
| b |
| Binary file test-data/faahKO-single-class.xset.merged.group.RData has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/faahKO-single-class.xset.merged.group.retcor.RData |
| b |
| Binary file test-data/faahKO-single-class.xset.merged.group.retcor.RData has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/faahKO-single-class.xset.merged.group.retcor.group.RData |
| b |
| Binary file test-data/faahKO-single-class.xset.merged.group.retcor.group.RData has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.RData |
| b |
| Binary file test-data/faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.RData has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData |
| b |
| Binary file test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html Mon Sep 11 09:14:35 2023 +0000 |
| [ |
| @@ -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> |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/faahKO.xset.group.dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/faahKO.xset.group.dataMatrix.tsv Mon Sep 11 09:14:35 2023 +0000 |
| b |
| b'@@ -0,0 +1,8373 @@\n+name\tko15\tko16\twt15\twt16\n+M200T2877\tNA\t506848.884266667\tNA\tNA\n+M200T3188\tNA\t4333.4849999999\tNA\tNA\n+M200T3483\t6029.94499999992\tNA\tNA\tNA\n+M200T3874\t1144.01499999999\tNA\tNA\tNA\n+M200T3672\tNA\tNA\t5108.15999999988\tNA\n+M200T3523\tNA\tNA\t4586.52650000006\tNA\n+M200T3980\tNA\tNA\tNA\t1242.61000000004\n+M200T3811\tNA\tNA\t1018.81499999998\tNA\n+M201T3548\tNA\t2863.6449999999\tNA\tNA\n+M201T3778\tNA\tNA\t1680.81000000006\tNA\n+M201T4055\tNA\tNA\t1339.64000000005\tNA\n+M201T3270\tNA\tNA\t4090.91000000014\tNA\n+M201T2559\tNA\t14307.2299999999\tNA\tNA\n+M201T3630\tNA\tNA\tNA\t2931.24499999993\n+M201T3141\tNA\t254581.758476187\tNA\tNA\n+M201T3991\tNA\tNA\t1657.33500000006\tNA\n+M201T3683\tNA\tNA\t2906.20499999993\tNA\n+M201T3802\tNA\tNA\tNA\t3245.80999999992\n+M201T3506\t4023.61499999999\tNA\tNA\tNA\n+M201T4059\tNA\tNA\t1275.47500000004\tNA\n+M201T3885\tNA\t1220.70000000004\tNA\tNA\n+M201T4040\tNA\tNA\tNA\t1220.69999999998\n+M201T3930\tNA\tNA\t1284.72816666668\tNA\n+M201T4157\tNA\t774.575999999962\tNA\tNA\n+M202T4013\tNA\tNA\t831.015000000029\tNA\n+M202T3852\t892.050000000031\tNA\tNA\tNA\n+M202T3298\t2759.095\tNA\tNA\tNA\n+M202T3285\tNA\t3872.96250000005\tNA\tNA\n+M202T3318\t3588.54500000001\tNA\tNA\tNA\n+M202T3170\t7682.58500000004\tNA\tNA\tNA\n+M202T4062\tNA\tNA\t754.233600000007\tNA\n+M202T3758\tNA\tNA\t1151.71733333335\tNA\n+M202T3375\t9879.84499999977\tNA\tNA\tNA\n+M202T4035\tNA\t688.600000000024\tNA\tNA\n+M202T3897\tNA\t841.96999999998\tNA\tNA\n+M202T4145\tNA\tNA\tNA\t732.419999999983\n+M202T3190\tNA\t3806.07999999999\tNA\tNA\n+M202T3267\t77227.3769090911\tNA\tNA\tNA\n+M202T4012\tNA\t1629.165\tNA\tNA\n+M202T3936\tNA\tNA\t1461.71\tNA\n+M202T2896\t36435.3079999996\tNA\tNA\tNA\n+M202T3295\tNA\tNA\tNA\t3372.57500000002\n+M203T4041\tNA\tNA\tNA\t978.124999999977\n+M203T3320\tNA\tNA\tNA\t1136.19000000004\n+M203T3310\tNA\t1694.89499999996\tNA\tNA\n+M203T3972\tNA\tNA\t2796.65500000002\tNA\n+M203T4143\tNA\t1020.37999999998\tNA\tNA\n+M203T3353\tNA\t2974.74816666671\tNA\tNA\n+M203T3794\tNA\t2690.23500000009\tNA\tNA\n+M203T3725\tNA\tNA\tNA\t3345.96999999992\n+M203T2683\tNA\tNA\tNA\t6346.07499999991\n+M203T4181\tNA\t804.409999999981\tNA\tNA\n+M203T3325\t3852.53759999981\tNA\tNA\tNA\n+M203T4060\tNA\tNA\tNA\t1550.91499999999\n+M204T3517\tNA\tNA\t967.169999999987\tNA\n+M204T4132\tNA\tNA\tNA\t793.455000000074\n+M204T3059\t3905.96266666662\tNA\tNA\tNA\n+M204T3661\t3002.85120000003\tNA\tNA\tNA\n+M204T4018\t1111.14999999999\tNA\tNA\tNA\n+M204T3838\tNA\tNA\t1676.11500000006\tNA\n+M204T4146\tNA\tNA\tNA\t1089.24000000004\n+M204T2625\tNA\tNA\t3518.12000000012\tNA\n+M204T3401\tNA\tNA\tNA\t1586.91\n+M204T4077\tNA\t1062.63500000004\tNA\tNA\n+M204T3706\tNA\tNA\tNA\t1446.05999999997\n+M204T3602\tNA\tNA\tNA\t1032.90000000004\n+M205T3580\tNA\tNA\tNA\t2466.43999999994\n+M205T2591\tNA\tNA\tNA\t9189.67999999988\n+M205T2788\t1924712.01585714\t1757150.9648\t2129885.09357143\t1634341.9855862\n+M205T4035\t2600.69759999987\tNA\tNA\tNA\n+M205T3778\t2777.8750000001\tNA\t5180.14999999997\tNA\n+M205T3756\tNA\tNA\t2425.44000000002\tNA\n+M205T3919\tNA\t3392.55866666671\tNA\tNA\n+M205T4057\tNA\tNA\t1198.79000000004\tNA\n+M206T4073\tNA\tNA\t793.454999999982\tNA\n+M206T3345\tNA\tNA\t641.649999999985\tNA\n+M206T3295\tNA\tNA\tNA\t1023.50999999998\n+M206T3093\tNA\tNA\tNA\t4682.47999999989\n+M206T3196\tNA\t10174.0649999999\tNA\tNA\n+M206T4099\t1685.41525000004\tNA\tNA\tNA\n+M206T2783\t213659.293920001\tNA\t253825.557279999\t241844.442068965\n+M206T3448\tNA\tNA\tNA\t3090.62812500006\n+M206T2539\tNA\tNA\t9324.27000000002\tNA\n+M206T3185\t1931.20999999997\tNA\tNA\tNA\n+M206T3433\tNA\tNA\tNA\t2558.77500000009\n+M206T3551\tNA\tNA\t3048.62\tNA\n+M206T3237\t1713.67500000006\tNA\tNA\tNA\n+M206T3262\tNA\tNA\tNA\t3137.82499999993\n+M206T3699\tNA\tNA\tNA\t1953.12000000007\n+M206T4052\tNA\tNA\tNA\t1505.46128571426\n+M206T3357\tNA\tNA\tNA\t1536.82999999996\n+M206T3674\tNA\tNA\tNA\t2237.94999999995\n+M206T3766\tNA\tNA\tNA\t2529.03999999997\n+M206T3777\tNA\tNA\tNA\t3962.32680000009\n+M206T3375\tNA\tNA\tNA\t2723.09999999996\n+M206T3300\tNA\tNA\tNA\t3643.31999999999\n+M207T3586\tNA\tNA\tNA\t6897.63840000006\n+M207T3137\tNA\t9225.67499999978\tNA\tNA\n+M207T2864\tNA\t12172.5700000004\tNA\tNA\n+M207T3771\tNA\tNA\tNA\t4175.41999999994\n+M207T3179\tNA\t6866.59314285725\tNA\tNA\n+M207T2719\tNA\t451863.663\t364609.769939392\t360908.933642857\n+M207T3796\t10555.4061538462\tNA\tNA\tNA\n+M207T4090\tNA\tNA\t2114.31500000007\tNA\n+M207T3603\t5669.9950000002\tNA\tNA\tNA\n+M207T3442\tNA\t50'..b'00000017\tNA\tNA\tNA\n+M596T2675\t2591.63999999996\tNA\tNA\tNA\n+M596T3182_2\tNA\tNA\tNA\t1197.07200000001\n+M597T3968\t5639.95966666667\tNA\tNA\tNA\n+M597T2545\tNA\t2941.96500000005\tNA\tNA\n+M597T2534\tNA\t3727.82999999995\tNA\tNA\n+M597T2551\tNA\tNA\tNA\t4759.16500000003\n+M597T2720\tNA\tNA\t4531.87800000008\tNA\n+M597T2589\t3938.68550000005\tNA\tNA\tNA\n+M597T2566\tNA\t2184.73999999997\tNA\tNA\n+M597T3071\tNA\tNA\t7801.52500000005\tNA\n+M597T3292\tNA\t6108.19500000008\tNA\tNA\n+M597T3478\tNA\t7109.79500000002\tNA\tNA\n+M597T3874\tNA\tNA\t1399.11000000005\tNA\n+M597T3664\t3813.49883333338\tNA\tNA\tNA\n+M597T3789\tNA\tNA\t9477.64000000033\tNA\n+M597T4082\tNA\tNA\t27582.3906250001\tNA\n+M597T2922\tNA\tNA\tNA\t3881.19999999991\n+M597T2539\tNA\tNA\tNA\t4424.01941666667\n+M597T2791\tNA\tNA\t23087.5229375002\tNA\n+M597T3021\tNA\t8213.12000000029\tNA\tNA\n+M597T3813\tNA\t1186500.84141178\tNA\tNA\n+M597T4130\t15187.814210526\tNA\tNA\tNA\n+M598T2652\tNA\tNA\tNA\t5450.66280000004\n+M598T2896\tNA\tNA\tNA\t2579.12000000009\n+M598T3985\t4690.30499999994\tNA\tNA\tNA\n+M598T3927\tNA\tNA\tNA\t5100.33500000001\n+M598T3852\tNA\tNA\t6475.97000000023\tNA\n+M598T4234\t780.835199999962\tNA\tNA\tNA\n+M598T3911\t2421.055\tNA\tNA\tNA\n+M598T2838\t4328.7899999999\tNA\tNA\tNA\n+M598T3866\tNA\tNA\t923.232000000008\tNA\n+M598T2735\tNA\tNA\t3392.92\tNA\n+M598T2526\tNA\tNA\t3350.66499999992\tNA\n+M598T3054\tNA\tNA\t3904.17600000003\tNA\n+M598T2564\tNA\tNA\t5259.96499999993\tNA\n+M598T3243\tNA\tNA\t11160.015\tNA\n+M598T3165\tNA\tNA\tNA\t1547.78500000005\n+M598T3688\tNA\tNA\tNA\t2907.39840000003\n+M598T3570\t4893.75500000017\tNA\tNA\tNA\n+M598T2990\tNA\t7907.94500000028\tNA\tNA\n+M598T3738\t6735.75999999984\tNA\tNA\tNA\n+M598T3730\tNA\t29323.4050000004\tNA\tNA\n+M598T3719\tNA\tNA\tNA\t48876.8056363635\n+M598T3850\tNA\t19344.1924374998\tNA\tNA\n+M598T4228_1\tNA\tNA\tNA\t852.92499999998\n+M598T3702\tNA\tNA\tNA\t28572.205000001\n+M598T3814\tNA\t201593.909999999\tNA\tNA\n+M598T3223\tNA\t16185.5021250003\tNA\tNA\n+M598T2827\t5337.7886250001\tNA\tNA\tNA\n+M598T3400\tNA\tNA\t4532.24000000016\tNA\n+M598T3487\tNA\tNA\t9308.62000000032\tNA\n+M598T3708\tNA\tNA\tNA\t65022.6200000009\n+M598T4228_2\t1558.64039999994\tNA\tNA\tNA\n+M598T3115\t3137.82499999993\tNA\tNA\tNA\n+M598T3371\tNA\tNA\tNA\t7501.04499999995\n+M598T3825\tNA\t126881.278714286\tNA\tNA\n+M598T2659\t2139.08160000002\tNA\tNA\tNA\n+M598T2680\tNA\t2826.02880000002\tNA\tNA\n+M598T3181\tNA\t2838.6076666667\tNA\tNA\n+M598T2534\tNA\t1600.99499999996\tNA\tNA\n+M598T2764\tNA\t5078.42499999999\tNA\tNA\n+M598T2952\t5756.0700000002\tNA\tNA\tNA\n+M598T4015\t4444.59999999997\tNA\tNA\tNA\n+M599T4234\tNA\tNA\tNA\t881.094999999979\n+M599T3187\tNA\tNA\tNA\t2164.39499999999\n+M599T2935\tNA\t2557.20999999994\tNA\tNA\n+M599T2855\tNA\tNA\tNA\t3757.56499999997\n+M599T2622\tNA\t2237.94999999995\tNA\tNA\n+M599T3096\tNA\tNA\tNA\t5745.1150000002\n+M599T2619\t24597.6221333335\tNA\tNA\tNA\n+M599T4179\tNA\tNA\t769.979999999982\tNA\n+M599T3744_1\tNA\t8220.94499999976\tNA\tNA\n+M599T2885\tNA\tNA\tNA\t3269.28500000002\n+M599T4196\t1370.93999999996\tNA\tNA\tNA\n+M599T4163\tNA\t8068.71033333314\tNA\t5823.36499999964\n+M599T3697\tNA\tNA\t55051.9369090907\tNA\n+M599T3980\tNA\t15327.6100000005\tNA\tNA\n+M599T3839\tNA\tNA\t5238.05500000018\tNA\n+M599T4129\tNA\tNA\t13849.6178571426\tNA\n+M599T3478\tNA\tNA\tNA\t6298.5500000001\n+M599T3719\t22852.13\tNA\tNA\tNA\n+M599T4048\t798856.451441174\tNA\t897286.005000001\tNA\n+M599T3929\tNA\tNA\tNA\t2271127.28014893\n+M599T3744_2\t2472129.73859259\tNA\tNA\tNA\n+M599T3731\tNA\tNA\t1909653.70493332\tNA\n+M599T3431\t35592.8437333336\tNA\tNA\tNA\n+M599T4130\tNA\tNA\tNA\t707685.939314288\n+M599T2847\tNA\t5415.77280000005\tNA\tNA\n+M599T3810\t79625.6350000028\tNA\tNA\tNA\n+M599T2974\tNA\tNA\tNA\t12502.4521250001\n+M599T4127\tNA\t354770.43852632\tNA\tNA\n+M599T3724\tNA\tNA\t797434.72246154\tNA\n+M600T3407\t3353.79499999992\tNA\tNA\tNA\n+M600T3005\tNA\t5849.96999999986\tNA\tNA\n+M600T2730\tNA\tNA\tNA\t1760.62499999996\n+M600T3609\tNA\tNA\tNA\t5001.73999999997\n+M600T2523\tNA\tNA\t3209.81499999996\tNA\n+M600T2562\tNA\t2928.1150000001\tNA\tNA\n+M600T2606\t6022.12000000021\tNA\tNA\t2331.63714285708\n+M600T2782\tNA\tNA\tNA\t2608.74386666668\n+M600T3449\t4671.52499999989\t8782.77999999999\tNA\tNA\n+M600T2542\tNA\t3639.80233333338\tNA\tNA\n+M600T3348\t2327.15500000008\tNA\tNA\tNA\n+M600T3207\t7784.31000000027\tNA\tNA\tNA\n+M600T3079\tNA\tNA\tNA\t3430.04160000003\n+M600T2846\tNA\tNA\tNA\t1987.33833333336\n+M600T2966\t9211.58999999991\tNA\tNA\tNA\n' |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 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 09:14:35 2023 +0000 |
| b |
| b'@@ -0,0 +1,8373 @@\n+name\tnamecustom\tmz\tmzmin\tmzmax\trt\trtmin\trtmax\tnpeaks\tKO\tWT\tpeakidx\tms_level\n+M200T2877\tM200.1T2877\t200.100006103516\t200.100006103516\t200.100006103516\t2876.967\t2876.967\t2876.967\t1\t1\t0\t2697\t1\n+M200T3188\tM200.2T3188.4\t200.199996948242\t200.199996948242\t200.199996948242\t3188.392\t3188.392\t3188.392\t1\t1\t0\t3054\t1\n+M200T3483\tM200.2T3482.6\t200.199996948242\t200.199996948242\t200.199996948242\t3482.604\t3482.604\t3482.604\t1\t1\t0\t1089\t1\n+M200T3874\tM200.2T3873.8\t200.199996948242\t200.199996948242\t200.199996948242\t3873.842\t3873.842\t3873.842\t1\t1\t0\t1677\t1\n+M200T3672\tM200.2T3672\t200.199996948242\t200.199996948242\t200.199996948242\t3671.963\t3671.963\t3671.963\t1\t0\t1\t6014\t1\n+M200T3523\tM200.2T3523.3\t200.199996948242\t200.199996948242\t200.199996948242\t3523.293\t3523.293\t3523.293\t1\t0\t1\t5859\t1\n+M200T3980\tM200.3T3980.3\t200.300003051758\t200.300003051758\t200.300003051758\t3980.259\t3980.259\t3980.259\t1\t0\t1\t8804\t1\n+M200T3811\tM200.3T3811.2\t200.300003051758\t200.300003051758\t200.300003051758\t3811.244\t3811.244\t3811.244\t1\t0\t1\t6249\t1\n+M201T3548\tM200.8T3548.3\t200.800003051758\t200.800003051758\t200.800003051758\t3548.332\t3548.332\t3548.332\t1\t1\t0\t3594\t1\n+M201T3778\tM200.8T3778.4\t200.800003051758\t200.800003051758\t200.800003051758\t3778.38\t3778.38\t3778.38\t1\t0\t1\t6185\t1\n+M201T4055\tM200.8T4055.4\t200.800003051758\t200.800003051758\t200.800003051758\t4055.377\t4055.377\t4055.377\t1\t0\t1\t6585\t1\n+M201T3270\tM200.9T3269.8\t200.900009155273\t200.900009155273\t200.900009155273\t3269.77\t3269.77\t3269.77\t1\t0\t1\t5484\t1\n+M201T2559\tM200.9T2559.3\t200.900009155273\t200.900009155273\t200.900009155273\t2559.281\t2559.281\t2559.281\t1\t1\t0\t2311\t1\n+M201T3630\tM200.9T3629.7\t200.900009155273\t200.900009155273\t200.900009155273\t3629.709\t3629.709\t3629.709\t1\t0\t1\t8310\t1\n+M201T3141\tM201.1T3141.4\t201.100006103516\t201.100006103516\t201.100006103516\t3141.444\t3141.444\t3141.444\t1\t1\t0\t3007\t1\n+M201T3991\tM201.2T3991.2\t201.199996948242\t201.199996948242\t201.199996948242\t3991.214\t3991.214\t3991.214\t1\t0\t1\t6528\t1\n+M201T3683\tM201.2T3682.9\t201.199996948242\t201.199996948242\t201.199996948242\t3682.918\t3682.918\t3682.918\t1\t0\t1\t6034\t1\n+M201T3802\tM201.2T3801.9\t201.199996948242\t201.199996948242\t201.199996948242\t3801.854\t3801.854\t3801.854\t1\t0\t1\t8577\t1\n+M201T3506\tM201.2T3506.1\t201.199996948242\t201.199996948242\t201.199996948242\t3506.078\t3506.078\t3506.078\t1\t1\t0\t1133\t1\n+M201T4059\tM201.2T4058.5\t201.199996948242\t201.199996948242\t201.199996948242\t4058.507\t4058.507\t4058.507\t1\t0\t1\t6593\t1\n+M201T3885\tM201.3T3884.8\t201.300003051758\t201.300003051758\t201.300003051758\t3884.797\t3884.797\t3884.797\t1\t1\t0\t4093\t1\n+M201T4040\tM201.3T4039.7\t201.300003051758\t201.300003051758\t201.300003051758\t4039.727\t4039.727\t4039.727\t1\t0\t1\t8870\t1\n+M201T3930\tM201.3T3930.2\t201.300003051758\t201.300003051758\t201.300003051758\t3930.18\t3930.18\t3930.18\t1\t0\t1\t6439\t1\n+M201T4157\tM201.3T4157.1\t201.300003051758\t201.300003051758\t201.300003051758\t4157.099\t4157.099\t4157.099\t1\t1\t0\t4557\t1\n+M202T4013\tM201.7T4013.1\t201.699996948242\t201.699996948242\t201.699996948242\t4013.123\t4013.123\t4013.123\t1\t0\t1\t6548\t1\n+M202T3852\tM201.7T3851.9\t201.699996948242\t201.699996948242\t201.699996948242\t3851.933\t3851.933\t3851.933\t1\t1\t0\t1623\t1\n+M202T3298\tM201.8T3297.9\t201.800003051758\t201.800003051758\t201.800003051758\t3297.939\t3297.939\t3297.939\t1\t1\t0\t832\t1\n+M202T3285\tM201.8T3285.4\t201.800003051758\t201.800003051758\t201.800003051758\t3285.419\t3285.419\t3285.419\t1\t1\t0\t3177\t1\n+M202T3318\tM201.8T3318.3\t201.800003051758\t201.800003051758\t201.800003051758\t3318.284\t3318.284\t3318.284\t1\t1\t0\t863\t1\n+M202T3170\tM201.8T3169.6\t201.800003051758\t201.800003051758\t201.800003051758\t3169.613\t3169.613\t3169.613\t1\t1\t0\t659\t1\n+M202T4062\tM201.8T4061.6\t201.800003051758\t201.800003051758\t201.800003051758\t4061.637\t4061.637\t4061.637\t1\t0\t1\t6595\t1\n+M202T3758\tM201.8T3758\t201.800003051758\t201.800003051758\t201.800003051758\t3758.036\t3758.036\t3758.036\t1\t0\t1\t6159\t1\n+M202T3375\tM201.8T3374.6\t201.800003051758\t201.800003051758\t201.800003051758\t3374.622\t3374.622\t3374.622\t1\t1\t0\t941\t1\n+M202T4035\tM201.9T4035\t201.900009155273\t201.900009155273\t201.900009155273\t4035.032\t4035.032\t40'..b'024414062\t3096.06\t3096.06\t3096.06\t1\t0\t1\t7627\t1\n+M599T2619\tM598.9T2618.8\t598.900024414062\t598.900024414062\t598.900024414062\t2618.75\t2618.75\t2618.75\t1\t1\t0\t93\t1\n+M599T4179\tM599T4179\t599\t599\t599\t4179.008\t4179.008\t4179.008\t1\t0\t1\t6828\t1\n+M599T3744_1\tM599.1T3744_1\t599.100036621094\t599.100036621094\t599.100036621094\t3743.951\t3743.951\t3743.951\t1\t1\t0\t3887\t1\n+M599T2885\tM599.1T2884.8\t599.100036621094\t599.100036621094\t599.100036621094\t2884.791\t2884.791\t2884.791\t1\t0\t1\t7424\t1\n+M599T4196\tM599.1T4196.2\t599.100036621094\t599.100036621094\t599.100036621094\t4196.223\t4196.223\t4196.223\t1\t1\t0\t2190\t1\n+M599T4163\tM599.2T4163.4\t599.200012207031\t599.200012207031\t599.200012207031\t4163.358\t4160.228\t4166.488\t2\t1\t1\t4567,9114\t1\n+M599T3697\tM599.2T3697\t599.200012207031\t599.200012207031\t599.200012207031\t3697.002\t3697.002\t3697.002\t1\t0\t1\t6075\t1\n+M599T3980\tM599.2T3980.3\t599.200012207031\t599.200012207031\t599.200012207031\t3980.259\t3980.259\t3980.259\t1\t1\t0\t4253\t1\n+M599T3839\tM599.2T3839.4\t599.200012207031\t599.200012207031\t599.200012207031\t3839.413\t3839.413\t3839.413\t1\t0\t1\t6302\t1\n+M599T4129\tM599.2T4128.9\t599.200012207031\t599.200012207031\t599.200012207031\t4128.93\t4128.93\t4128.93\t1\t0\t1\t6764\t1\n+M599T3478\tM599.2T3477.9\t599.200012207031\t599.200012207031\t599.200012207031\t3477.909\t3477.909\t3477.909\t1\t0\t1\t8116\t1\n+M599T3719\tM599.2T3718.9\t599.200012207031\t599.200012207031\t599.200012207031\t3718.912\t3718.912\t3718.912\t1\t1\t0\t1427\t1\n+M599T4048\tM599.3T4047.6\t599.299987792969\t599.299987792969\t599.299987792969\t4047.552\t4047.552\t4053.812\t3\t1\t1\t1980,6571,6597\t1\n+M599T3929\tM599.3T3928.6\t599.299987792969\t599.299987792969\t599.299987792969\t3928.615\t3928.615\t3928.615\t2\t0\t1\t8717,8748\t1\n+M599T3744_2\tM599.3T3744_2\t599.299987792969\t599.299987792969\t599.299987792969\t3743.951\t3743.951\t3743.951\t1\t1\t0\t1481\t1\n+M599T3731\tM599.3T3731.4\t599.299987792969\t599.299987792969\t599.299987792969\t3731.431\t3731.431\t3731.431\t1\t0\t1\t6133\t1\n+M599T3431\tM599.3T3431\t599.299987792969\t599.299987792969\t599.299987792969\t3430.96\t3430.96\t3430.96\t1\t1\t0\t1028\t1\n+M599T4130\tM599.3T4130.5\t599.299987792969\t599.299987792969\t599.299987792969\t4130.494\t4130.494\t4130.494\t1\t0\t1\t9058\t1\n+M599T2847\tM599.4T2847.2\t599.400024414062\t599.400024414062\t599.400024414062\t2847.232\t2847.232\t2847.232\t1\t1\t0\t2616\t1\n+M599T3810\tM599.4T3809.7\t599.400024414062\t599.400024414062\t599.400024414062\t3809.679\t3809.679\t3809.679\t1\t1\t0\t1552\t1\n+M599T2974\tM599.4T2974\t599.400024414062\t599.400024414062\t599.400024414062\t2973.994\t2973.994\t2973.994\t1\t0\t1\t7528\t1\n+M599T4127\tM599.4T4127.4\t599.400024414062\t599.400024414062\t599.400024414062\t4127.364\t4127.364\t4127.364\t1\t1\t0\t4466\t1\n+M599T3724\tM599.4T3723.6\t599.400024414062\t599.400024414062\t599.400024414062\t3723.607\t3723.607\t3723.607\t1\t0\t1\t6112\t1\n+M600T3407\tM599.5T3407.5\t599.5\t599.5\t599.5\t3407.486\t3407.486\t3407.486\t1\t1\t0\t999\t1\n+M600T3005\tM599.5T3005.3\t599.5\t599.5\t599.5\t3005.293\t3005.293\t3005.293\t1\t1\t0\t2885\t1\n+M600T2730\tM599.5T2729.9\t599.5\t599.5\t599.5\t2729.861\t2729.861\t2729.861\t1\t0\t1\t7235\t1\n+M600T3609\tM599.5T3609.4\t599.5\t599.5\t599.5\t3609.365\t3609.365\t3609.365\t1\t0\t1\t8294\t1\n+M600T2523\tM599.8T2523.3\t599.799987792969\t599.799987792969\t599.799987792969\t2523.287\t2523.287\t2523.287\t1\t0\t1\t4673\t1\n+M600T2562\tM599.8T2562.4\t599.799987792969\t599.799987792969\t599.799987792969\t2562.411\t2562.411\t2562.411\t1\t1\t0\t2316\t1\n+M600T2606\tM599.9T2606.2\t599.900024414062\t599.900024414062\t599.900024414062\t2606.23\t2604.665\t2607.795\t2\t1\t1\t75,7054\t1\n+M600T2782\tM599.9T2781.5\t599.900024414062\t599.900024414062\t599.900024414062\t2781.504\t2781.504\t2781.504\t1\t0\t1\t7290\t1\n+M600T3449\tM600T3449\t600\t600\t600\t3448.9575\t3445.045\t3452.87\t2\t2\t0\t1049,3394\t1\n+M600T2542\tM600T2542.1\t600\t600\t600\t2542.067\t2542.067\t2542.067\t1\t1\t0\t2295\t1\n+M600T3348\tM600T3348\t600\t600\t600\t3348.018\t3348.018\t3348.018\t1\t1\t0\t903\t1\n+M600T3207\tM600T3207.2\t600\t600\t600\t3207.172\t3207.172\t3207.172\t1\t1\t0\t705\t1\n+M600T3079\tM600T3078.8\t600\t600\t600\t3078.845\t3078.845\t3078.845\t1\t0\t1\t7609\t1\n+M600T2846\tM600T2845.7\t600\t600\t600\t2845.667\t2845.667\t2845.667\t1\t0\t1\t7388\t1\n+M600T2966\tM600T2966.2\t600\t600\t600\t2966.169\t2966.169\t2966.169\t1\t1\t0\t455\t1\n' |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/faahKO_reduce.zip |
| b |
| Binary file test-data/faahKO_reduce.zip has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/ko15-raw.RData |
| b |
| Binary file test-data/ko15-raw.RData has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/ko15.CDF |
| b |
| Binary file test-data/ko15.CDF has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/ko16-raw.RData |
| b |
| Binary file test-data/ko16-raw.RData has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/ko16.CDF |
| b |
| Binary file test-data/ko16.CDF has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/roiList.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/roiList.txt Mon Sep 11 09:14:35 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +scmin scmax mzmin mzmax length intensity +200 300 300 350 100 5000 |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/sampleMetadata.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampleMetadata.tab Mon Sep 11 09:14:35 2023 +0000 |
| b |
| @@ -0,0 +1,6 @@ +wt16 WT +ko16 KO +wt15 WT +ko15 KO +ko10 KO +foobar01 FOOBAR |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampleMetadata.tsv Mon Sep 11 09:14:35 2023 +0000 |
| b |
| @@ -0,0 +1,5 @@ +sample_name class +ko15 KO +ko16 KO +wt15 WT +wt16 WT |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/sampleMetadata_missing.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampleMetadata_missing.tab Mon Sep 11 09:14:35 2023 +0000 |
| b |
| @@ -0,0 +1,5 @@ +wt16 WT +wt15 WT +ko15 KO +ko10 KO +foobar01 FOOBAR |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/wt15-raw.RData |
| b |
| Binary file test-data/wt15-raw.RData has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/wt15.CDF |
| b |
| Binary file test-data/wt15.CDF has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/wt16-raw.RData |
| b |
| Binary file test-data/wt16-raw.RData has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 test-data/wt16.CDF |
| b |
| Binary file test-data/wt16.CDF has changed |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 xcms_export_samplemetadata.r --- a/xcms_export_samplemetadata.r Wed Apr 07 09:53:54 2021 +0000 +++ b/xcms_export_samplemetadata.r Mon Sep 11 09:14:35 2023 +0000 |
| [ |
| @@ -2,26 +2,28 @@ #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") loadAndDisplayPackages(pkgs) -cat("\n\n"); +cat("\n\n") args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects sampleMetadata <- NULL for (image in args$images) { - load(image) - if (exists("raw_data")) xdata <- raw_data - 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.*") - if (is.null(sampleMetadata)) - sampleMetadata <- xdata@phenoData@data - else - sampleMetadata <- rbind(sampleMetadata, xdata@phenoData@data) + load(image) + if (exists("raw_data")) xdata <- raw_data + 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.*") + if (is.null(sampleMetadata)) + sampleMetadata <- xdata@phenoData@data + else + sampleMetadata <- rbind(sampleMetadata, xdata@phenoData@data) } colnames(sampleMetadata) <- c("sample_name", "class") sampleMetadata$sample_name <- make.names(sampleMetadata$sample_name) |
| b |
| diff -r 94eb263cfab4 -r cdab04a1d1d7 xcms_export_samplemetadata.xml --- a/xcms_export_samplemetadata.xml Wed Apr 07 09:53:54 2021 +0000 +++ b/xcms_export_samplemetadata.xml Mon Sep 11 09:14:35 2023 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="xcms_export_samplemetadata" name="xcms get a sampleMetadata file" version="@TOOL_VERSION@+galaxy0"> +<tool id="xcms_export_samplemetadata" name="xcms get a sampleMetadata file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>which need to be filled with extra information</description> <macros> @@ -112,6 +112,8 @@ Blanc09 blank =========================== ============ +@HELP_XCMS_MANUAL@ + --------------------------------------------------- Changelog/News |
