| Previous changeset 32:b02d1992a43a (2021-04-07) Next changeset 34:6550698fe60f (2024-07-15) |
|
Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e |
|
modified:
abims_xcms_xcmsSet.xml lib.r macros_xcms.xml xcms_xcmsSet.r |
|
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_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 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-xset.RData test-data/ko16-raw.RData test-data/ko16-xset.RData test-data/ko16.CDF test-data/noclass.merged.sampleMetadata.tsv 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/wt15.CDF test-data/wt16-raw.RData test-data/wt16-xset.RData test-data/wt16.CDF |
|
removed:
README.rst destinations_input_type.py job_conf.xml.sample repository_dependencies.xml |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 README.rst --- a/README.rst Wed Apr 07 16:47:14 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -Job Dynamic Destination Mapping -------------------------------- - -**Why** - -xcmsSet wrapper allow both individual file and zip file which can contain several samples. -Thus, it can be interesting to adjust the number of thread according to the input type. -For example: 1 thread for a single mzXML or NetCDF file and 8 threads for a zip file. - -**What** - -The [Dynamic Destination Mapping](https://galaxyproject.org/admin/config/jobs/#dynamic-destination-mapping) allow Galaxy to choose a destination at runtime based on factors such as the job inputs, user submitting the job, cluster status, etc... - -**How** - -1. The file [`destinations_input_type.py`](https://raw.githubusercontent.com/workflow4metabolomics/xcms/master/galaxy/xcms_xcmsset/destinations_input_type.py) (shiped with this tool) must be place in `lib/galaxy/jobs/rules/` -2. The `job_conf.xml` must be inspired by the [`job_conf.xml.sample`](https://github.com/workflow4metabolomics/xcms/blob/master/galaxy/xcms_xcmsset/job_conf.xml.sample) shiped with this tool -3. The final destination names must match between the `job_conf.xml` and the `destinations_input_type.py` -4. Restart Galaxy - - -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 3.4.4.1 - 30/04/2019** - -- BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms. - -**Version 3.4.4.0 - 08/02/2019** - -- UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) - -**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: Spectra Filters (previously scanrange), CentWave.(mzCenterFun, fitgauss, verboseColumns), MatchedFilter.(sigma, impute, baseValue, max), MSW.(verboseColumns), ... - -- UPDATE: since xcms 3.0.0, some options are no more available: scanrange (replace by filters), profmethod, MatchedFilter.step, MatchedFilter.sigma, MSW.winSize.noise, MSW.SNR.method - -- IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values. - -- IMPROVEMENT: the tool "should" be now more flexible in term of file naming: it "should" accept space and comma. But don't be too imaginative :) - -- CHANGE: removing of the TIC and BPC plots. You can new use the dedicated tool "xcms plot chromatogram" - - -**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 - 22/02/2017** - -- NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group". - -- BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1 - - -**Version 2.0.11 - 22/12/2016** - -- BUGFIX: propose scanrange for all methods - - -**Version 2.0.10 - 22/12/2016** - -- BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph - - -**Version 2.0.9 - 06/07/2016** - -- UPGRADE: upgrade the xcms version from 1.44.0 to 1.46.0 - - -**Version 2.0.8 - 06/04/2016** - -- TEST: refactoring to pass planemo test using conda dependencies - - -**Version 2.0.7 - 10/02/2016** - -- BUGFIX: better management of errors. Datasets remained green although the process failed - -- BUGFIX/IMPROVEMENT: New checking steps around the imported data in order to raise explicte error message before or after launch XCMS: checking of bad characters in the filenames, checking of the XML integrity and checking of duplicates which can appear in the sample names during the XCMS process because of bad characters - -- BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer - -- UPDATE: refactoring of internal management of inputs/outputs - -- TEST: refactoring to feed the new report tool - - -**Version 2.0.2 - 18/01/2016** - -- BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases. - - -**Version 2.0.2 - 09/10/2015** - -- BUGFIX: Some users reported a bug in xcms.xcmsSet. The preprocessing stops itself and doesn't import the whole dataset contained in the zip file without warning. But meanwhile, please check your samplemetadata dataset and the number of rows. - - -**Version 2.0.2 - 02/06/2015** - -- NEW: The W4M workflows will now take as input a zip file to ease the transfer and to improve dataset exchange between tools and users. (See How_to_upload). The previous "Library directory name" is still available but we invite user to switch on the new zip system as soon as possible. - -- 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. |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 abims_xcms_xcmsSet.xml --- a/abims_xcms_xcmsSet.xml Wed Apr 07 16:47:14 2021 +0000 +++ b/abims_xcms_xcmsSet.xml Mon Sep 11 09:22:36 2023 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy0"> +<tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Chromatographic peak detection</description> <macros> @@ -187,11 +187,8 @@ <outputs> <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.xset.RData" from_work_dir="xcmsSet.RData" /> <data name="log" format="txt" label="${image.name.rsplit('.',1)[0]}.xset.log.txt" from_work_dir="log.txt" /> - <data name="peaklist_out1" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" > - <filter>methods['method'] == 'CentWave' and (methods['CentWaveAdv']['peaklist'])</filter> - </data> - <data name="peaklist_out2" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" > - <filter>methods['method'] == 'MatchedFilter' and (methods['MatchedFilterAdv']['peaklist'])</filter> + <data name="peaklist_out" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" > + <filter>methods['method'] in ['CentWave', 'MatchedFilter'] and (methods['CentWaveAdv']['peaklist'])</filter> </data> </outputs> @@ -227,7 +224,7 @@ <has_text text="Sample classes: KO, WT" /> </assert_stdout> </test>--> - <test> + <test expect_num_outputs="2"> <param name="image" value="ko15-raw.RData" ftype="rdata" /> <conditional name="methods"> <param name="method" value="CentWave" /> |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 destinations_input_type.py --- a/destinations_input_type.py Wed Apr 07 16:47:14 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,28 +0,0 @@ -import logging - - -''' -This file must be placed in lib/galaxy/jobs/rules/ -''' - - -def input_type(job): - ''' - This function checks the input file format/extension and decide which - destination in the job_conf.xml using - - If it's a zip file, we will launch the job in multi-thread mode - (-pe thread 8) - - If it's an individual file (mzxml, mzml, mzdata or netcdf), - the job will use for instance (-pe thread 1) - ''' - log = logging.getLogger(__name__) - indata = dict([(da.name, da.dataset) for da in job.input_datasets]) - indata.update([(da.name, da.dataset) for da in job.input_library_datasets]) - input_extension = indata["input"].extension - if 'input' in indata: - input_extension = indata["input"].extension - log.debug("The input extension is %s" % input_extension) - if input_extension in ["mzxml", "mzml", "mzdata", "netcdf"]: - return 'thread1-mem_free8' - # zip file - return 'thread8-mem_free16' |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 job_conf.xml.sample --- a/job_conf.xml.sample Wed Apr 07 16:47:14 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,33 +0,0 @@ -<?xml version="1.0"?> -<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> -<job_conf> - <plugins> - <plugin id="sge" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" type="runner"/> - <plugin id="dynamic" type="runner" > - <param id="rules_module">galaxy.jobs.rules</param> - </plugin> - </plugins> - <handlers> - <handler id="main"/> - </handlers> - <destinations default="sge_default"> - <destination id="sge_default" runner="sge"> - <param id="nativeSpecification">-V -w n -q galaxy.q</param> - </destination> - - <destination id="thread1-men_free8" runner="sge"> - <param id="nativeSpecification">-V -w n -q galaxy.q -pe thread 1 -R y -l mem_free=8G </param> - </destination> - <destination id="thread8-men_free12" runner="sge"> - <param id="nativeSpecification">-V -w n -q galaxy.q -pe thread 8 -R y -l mem_free=16G </param> - </destination> - - <destination id="python_destination_input_type" runner="dynamic"> - <param id="type">python</param> - <param id="function">input_type</param> - </destination> - </destinations> - <tools> - <tool destination="python_destination_input_type" id="abims_xcms_xcmsSet" /> - </tools> -</job_conf> |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 lib.r --- a/lib.r Wed Apr 07 16:47:14 2021 +0000 +++ b/lib.r Mon Sep 11 09:22:36 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 b02d1992a43a -r f5d51091cf84 macros_xcms.xml --- a/macros_xcms.xml Wed Apr 07 16:47:14 2021 +0000 +++ b/macros_xcms.xml Mon Sep 11 09:22:36 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 b02d1992a43a -r f5d51091cf84 repository_dependencies.xml --- a/repository_dependencies.xml Wed Apr 07 16:47:14 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 b02d1992a43a -r f5d51091cf84 static/images/msnbase_readmsdata_workflow.png |
| b |
| Binary file static/images/msnbase_readmsdata_workflow.png has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 static/images/xcms_fillpeaks_workflow.png |
| b |
| Binary file static/images/xcms_fillpeaks_workflow.png has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 static/images/xcms_group.png |
| b |
| Binary file static/images/xcms_group.png has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 static/images/xcms_group_workflow.png |
| b |
| Binary file static/images/xcms_group_workflow.png has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 static/images/xcms_merge_workflow.png |
| b |
| Binary file static/images/xcms_merge_workflow.png has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 static/images/xcms_plot_chromatogram_workflow.png |
| b |
| Binary file static/images/xcms_plot_chromatogram_workflow.png has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 static/images/xcms_retcor.png |
| b |
| Binary file static/images/xcms_retcor.png has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 static/images/xcms_retcor_workflow.png |
| b |
| Binary file static/images/xcms_retcor_workflow.png has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 static/images/xcms_summary_workflow.png |
| b |
| Binary file static/images/xcms_summary_workflow.png has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 test-data/BPIs.pdf |
| b |
| Binary file test-data/BPIs.pdf has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 test-data/MM14.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MM14.mzML Mon Sep 11 09:22:36 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 b02d1992a43a -r f5d51091cf84 test-data/TICs.pdf |
| b |
| Binary file test-data/TICs.pdf has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 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 09:22:36 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 b02d1992a43a -r f5d51091cf84 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 09:22:36 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 b02d1992a43a -r f5d51091cf84 test-data/faahKO-single-class.xset.merged.RData |
| b |
| Binary file test-data/faahKO-single-class.xset.merged.RData has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 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 b02d1992a43a -r f5d51091cf84 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 b02d1992a43a -r f5d51091cf84 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 b02d1992a43a -r f5d51091cf84 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 b02d1992a43a -r f5d51091cf84 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 b02d1992a43a -r f5d51091cf84 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 09:22:36 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 b02d1992a43a -r f5d51091cf84 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 09:22:36 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 b02d1992a43a -r f5d51091cf84 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 09:22:36 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 b02d1992a43a -r f5d51091cf84 test-data/faahKO_reduce.zip |
| b |
| Binary file test-data/faahKO_reduce.zip has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 test-data/ko15-xset.RData |
| b |
| Binary file test-data/ko15-xset.RData has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 test-data/ko16-raw.RData |
| b |
| Binary file test-data/ko16-raw.RData has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 test-data/ko16-xset.RData |
| b |
| Binary file test-data/ko16-xset.RData has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 test-data/ko16.CDF |
| b |
| Binary file test-data/ko16.CDF has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 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 09:22:36 2023 +0000 |
| b |
| @@ -0,0 +1,5 @@ +sample_name class +ko15 . +ko16 . +wt15 . +wt16 . |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 test-data/sampleMetadata.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampleMetadata.tab Mon Sep 11 09:22:36 2023 +0000 |
| b |
| @@ -0,0 +1,6 @@ +wt16 WT +ko16 KO +wt15 WT +ko15 KO +ko10 KO +foobar01 FOOBAR |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 test-data/sampleMetadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampleMetadata.tsv Mon Sep 11 09:22:36 2023 +0000 |
| b |
| @@ -0,0 +1,5 @@ +sample_name class +ko15 KO +ko16 KO +wt15 WT +wt16 WT |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 test-data/sampleMetadata_missing.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampleMetadata_missing.tab Mon Sep 11 09:22:36 2023 +0000 |
| b |
| @@ -0,0 +1,5 @@ +wt16 WT +wt15 WT +ko15 KO +ko10 KO +foobar01 FOOBAR |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 test-data/wt15-raw.RData |
| b |
| Binary file test-data/wt15-raw.RData has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 test-data/wt15-xset.RData |
| b |
| Binary file test-data/wt15-xset.RData has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 test-data/wt15.CDF |
| b |
| Binary file test-data/wt15.CDF has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 test-data/wt16-raw.RData |
| b |
| Binary file test-data/wt16-raw.RData has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 test-data/wt16-xset.RData |
| b |
| Binary file test-data/wt16-xset.RData has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 test-data/wt16.CDF |
| b |
| Binary file test-data/wt16.CDF has changed |
| b |
| diff -r b02d1992a43a -r f5d51091cf84 xcms_xcmsSet.r --- a/xcms_xcmsSet.r Wed Apr 07 16:47:14 2021 +0000 +++ b/xcms_xcmsSet.r Mon Sep 11 09:22:36 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") 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") @@ -34,7 +36,7 @@ #saving the commun parameters BPPARAM <- MulticoreParam(1) if (!is.null(args$BPPARAM)) { - BPPARAM <- MulticoreParam(args$BPPARAM) + BPPARAM <- MulticoreParam(args$BPPARAM) } register(BPPARAM) @@ -47,9 +49,9 @@ method <- args$method if (!is.null(args$roiList)) { - cat("\t\troiList provided\n") - args$roiList <- list(getDataFrameFromFile(args$roiList)) - print(args$roiList) + cat("\t\troiList provided\n") + args$roiList <- list(getDataFrameFromFile(args$roiList)) + print(args$roiList) } cat("\n\n") @@ -103,7 +105,7 @@ if (exists("peaklistParam")) { if (peaklistParam) { cat("\nCreating the chromatographic peaks' table...\n") - write.table(chromPeaks(xdata), file = "chromPeak_table.tsv", sep = "\t", quote = F, row.names = F) + write.table(chromPeaks(xdata), file = "chromPeak_table.tsv", sep = "\t", quote = FALSE, row.names = FALSE) } } |
