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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712 |
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added:
abims_xcms_retcor.xml xcms_retcor.r |
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removed:
abims_xcms_refine.xml xcms_refine.r |
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| diff -r 36480435e92b -r 8242376d9f35 abims_xcms_refine.xml --- a/abims_xcms_refine.xml Mon Sep 11 09:21:15 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,264 +0,0 @@\n-<tool id="abims_xcms_refine" name="xcms refineChromPeaks (refine)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n-\n- <description>Remove or merge chromatographic peaks based on specific criteria.</description>\n-\n- <macros>\n- <import>macros.xml</import>\n- <import>macros_xcms.xml</import>\n- </macros>\n-\n- <expand macro="requirements"/>\n-\n- <expand macro="stdio"/>\n-\n- <command><![CDATA[\n- @COMMAND_RSCRIPT@/xcms_refine.r\n- image \'$image\'\n-\n- method $methods.method\n- #if $methods.method == "CleanPeaks":\n- maxPeakwidth $methods.maxPeakwidth\n- #elif $methods.method == "FilterIntensity":\n- threshold $methods.threshold\n- nValues $methods.nValues\n- value $methods.value\n- #else:\n- expandRt $methods.expandRt\n- expandMz $methods.expandMz\n- ppm $methods.ppm\n- minProp $methods.minProp\n- #end if\n-\n- msLevel $msLevel\n-\n- @COMMAND_FILE_LOAD@\n-\n- @COMMAND_LOG_EXIT@\n- ]]></command>\n-\n- <inputs>\n- <param name="image" type="data" format="rdata.xcms.findchrompeaks" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks" />\n- <conditional name="methods">\n- <param name="method" type="select" label="Method for peak refinement" help="See the help section below">\n- <option value="CleanPeaks" selected="true">CleanPeaks - remove peaks that are too wide</option>\n- <option value="FilterIntensity">FilterIntensity - remove peaks with too low intensity</option>\n- <option value="MergeNeighboringPeaks">MergeNeighboringPeaks - combine peaks that are too close together</option>\n- </param>\n- <when value="CleanPeaks">\n- <param argument="maxPeakwidth" type="float" value="10" label="MaxPeakWidth" help="maximum peak width in seconds. See CleanPeaks manual (linked in help below)." />\n- </when>\n- <when value="FilterIntensity">\n- <param argument="threshold" type="float" value="0" label="minimal required intensity" help="minimal required intensity for a peak to be retained. Defaults to 0.0." />\n- <param argument="nValues" type="integer" value="1" label="minimum number of data points per peak" help="number of data points (per chromatographic peak) that have to be >= threshold. Defaults to 1." />\n- <param name="value" type="select" label="Definition of peak intensity" help="See the FilterIntensity manual (linked in help below). \'intb\' requires centWave processed data">\n- <option value="maxo" selected="true">maxo - use maximum peak intensities</option>\n- <option value="into">into - use integrated peak intensities</option>\n- <option value="intb">intb - use baseline-corrected integrated peak intensities</option>\n- </param>\n- </when>\n- <when value="MergeNeighboringPeaks">\n- <param argument="expandRt" type="float" value="2" label="rt expansion (seconds)" help="seconds of expansion of retention time window (on both sides) to check for overlapping peaks. Defaults to 2." />\n- <param argument="expandMz" type="float" value="0" label="m/z expansion (m/z units)" help="\'m/z units\' of expansion of m/z window (on both sides) to check for overlapping peaks. Defaults to 0." />\n- <param argument="ppm" type="float" value="10" label="ppm expansion (ppm units)" help="\'relative \'m/z units\' (in parts per million) of expansion of m/z window (on both sides) to check for overlapping peaks. Defaults to 10." />\n- <param argument="minProp" type="float" value="0.75" label="minimum proportion at midpoint" help="See MergeNeighboringPeaks manual (linked in help below). Minimum proportion midway between peaks relative to the smaller '..b': infomark\n-\n-**Authors** Johannes Rainer Johannes.Rainer@eurac.edu and Mar Garcia-Aloy mar.garcia@fmach.it\n-\n-@HELP_AUTHORS_WRAPPERS@\n-\n----------------------------------------------------\n-\n-\n-=====================\n-xcms refineChromPeaks\n-=====================\n-\n------------\n-Description\n------------\n-\n-After peak identification with xcms findChromPeaks (xcmsSet), this tool refines those peaks.\n-It either removes peaks that are too wide or removes peaks with too low intensity or combines peaks that are too close together.\n-\n-Note well that refineChromPeaks methods will always remove feature definitions,\n-because a call to this method can change or remove identified chromatographic peaks, which may be part of features.\n-Therefore it must only be run immediately after findChromPeaks (xcmsSet).\n-\n------------------\n-Workflow position\n------------------\n-\n-**Upstream tools**\n-\n-==================================== ======================== ==============================\n-Name Output file Format\n-==================================== ======================== ==============================\n-xcms.findChromPeaks Merger (single) xset.merged.RData rdata.xcms.findchrompeaks\n------------------------------------- ------------------------ ------------------------------\n-xcms.findChromPeaks (zip) ``*``.raw.xset.RData rdata.xcms.findchrompeaks\n-==================================== ======================== ==============================\n-\n-\n-**Downstream tools**\n-\n-==================================== ======================== =========================\n-Name Output file Format\n-==================================== ======================== =========================\n-xcms.findChromPeaks Merger (single) ``*``.raw.xset.RData rdata.xcms.findchrompeaks\n------------------------------------- ------------------------ -------------------------\n-xcms.groupChromPeaks (zip) ``*``.raw.xset.RData rdata.xcms.findchrompeaks\n-==================================== ======================== =========================\n-\n-**General schema of the metabolomic workflow**\n-\n-This tool would appear between findChromPeaks and group, but only when the choice of peaks needs to be refined, e.g., to accommodate HILIC data.\n-\n----------------------------------------------------\n-\n-----------\n-Parameters\n-----------\n-\n-Method to use for refinement\n-----------------------------\n-\n-**CleanPeaks**\n-\n- | Remove chromatographic peaks with too large rt width.\n- | See the CleanPeaks_manual_\n-\n-**FilterIntensity**\n-\n- | Remove chromatographic peaks based on intensity.\n- | See the FilterIntensity_manual_\n-\n-**MergeNeighboringPeaks**\n-\n- | Merge neighboring and overlapping chromatographic peaks.\n- | See the MergeNeighboringPeaks_manual_\n-\n-.. _CleanPeaks_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-clean.html\n-.. _FilterIntensity_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-filter-intensity.html\n-.. _MergeNeighboringPeaks_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-merge.html\n-\n-@HELP_XCMS_MANUAL@\n-\n-------------\n-Output files\n-------------\n-\n-xset.RData: rdata.xcms.findchrompeaks format\n-\n- | (single) RData files that are necessary in the second step of the workflow "xcms.groupChromPeaks" - must be merged first using "xcms.findChromPeaks Merger"\n- | (zip) RData file that is necessary in the second step of the workflow "xcms.groupChromPeaks".\n-\n-\n----------------------------------------------------\n-\n-Changelog/News\n---------------\n-\n-.. _news: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS\n-\n-\n-**Version 3.6.1.0 - 08/02/2021**\n-\n-- NEW: first version of tool wrapper\n-\n-\n- ]]></help>\n-\n- <citations>\n- <citation type="doi">10.5281/zenodo.3909299</citation>\n- <expand macro="citation_w4m"/>\n- <citation type="doi">10.1021/ac051437y</citation>\n- </citations>\n-\n-\n-</tool>\n' |
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| diff -r 36480435e92b -r 8242376d9f35 abims_xcms_retcor.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_xcms_retcor.xml Thu Mar 14 15:35:44 2024 +0000 |
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| b'@@ -0,0 +1,383 @@\n+<tool id="abims_xcms_retcor" name="xcms adjustRtime (retcor)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+\n+ <description>Retention Time Correction</description>\n+\n+ <macros>\n+ <import>macros.xml</import>\n+ <import>macros_xcms.xml</import>\n+ </macros>\n+\n+ <expand macro="requirements"/>\n+ <expand macro="stdio"/>\n+\n+ <command><![CDATA[\n+ @COMMAND_RSCRIPT@/xcms_retcor.r\n+ image \'$image\'\n+\n+ method $methods.method\n+ #if $methods.method == "PeakGroups":\n+ minFraction $methods.minFraction\n+ extraPeaks $methods.extraPeaks\n+ smooth $methods.smooth_cond.smooth\n+ ## PeakGroupsSmoothLoess Advanced\n+ span $methods.smooth_cond.PeakGroupsSmoothLoessAdv.span\n+ family $methods.smooth_cond.PeakGroupsSmoothLoessAdv.family\n+ #else\n+ binSize $methods.binSize\n+ ## Advanced\n+ #if $methods.ObiwarpAdv.centerSample != "":\n+ centerSample $methods.ObiwarpAdv.centerSample\n+ #end if\n+ response $methods.ObiwarpAdv.response\n+ distFun $methods.ObiwarpAdv.distFunCond.distFun\n+ gapInit $methods.ObiwarpAdv.distFunCond.gapInit\n+ gapExtend $methods.ObiwarpAdv.distFunCond.gapExtend\n+ factorDiag $methods.ObiwarpAdv.factorDiag\n+ factorGap $methods.ObiwarpAdv.factorGap\n+ localAlignment $methods.ObiwarpAdv.localAlignmentCond.localAlignment\n+ initPenalty $methods.ObiwarpAdv.localAlignmentCond.initPenalty\n+ #end if\n+\n+ @COMMAND_FILE_LOAD@\n+\n+ @COMMAND_LOG_EXIT@\n+ ]]></command>\n+\n+ <inputs>\n+ <param name="image" type="data" format="rdata.xcms.findchrompeaks,rdata.xcms.group,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks" />\n+ <conditional name="methods">\n+ <param name="method" type="select" label="Method to use for retention time correction" help="See the help section below" >\n+ <option value="PeakGroups" selected="true">PeakGroups - retention time correction based on aligment of features (peak groups) present in most/all samples.</option>\n+ <option value="Obiwarp">Obiwarp - alignment based on the complete mz-rt data.</option>\n+ </param>\n+ <when value="PeakGroups">\n+ <param argument="minFraction" type="float" value="0.9" min="0" max="1" label="Minimum required fraction of samples in which peaks for the peak group were identified" help="(previously missing)"/>\n+ <param argument="extraPeaks" type="integer" value="1" label="Maximal number of additional peaks for all samples to be assigned to a peak group for retention time correction" help="For a data set with 6 samples, \xe2\x80\x98extraPeaks = 1\xe2\x80\x99 uses all peak groups with a total peak count lower or equal to \xe2\x80\x986 + 1\xe2\x80\x99. The total peak count is the total number of peaks being assigned to a peak group and considers also multiple peaks within a sample being assigned to the group. (previously extra)" />\n+ <conditional name="smooth_cond">\n+ <param argument="smooth" type="select" label="Smooth method" >\n+ <option value="loess" selected="true">loess - non-linear alignment</option>\n+ <option value="linear">linear - linear alignment</option>\n+ </param>\n+ <when value="loess">\n+ <section name="PeakGroupsSmoothLoessAdv" title="Advanced Options" expanded="False">\n+ <param argument="span" type="float" value="0.2" label="Degree of smoothing for the loess fitting" />\n+ <param argument="family" type="select" label="Family" help="if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with T'..b'tention time adjustment based on the alignment of chromatographic peak groups present in all/most samples (hence corresponding to house keeping compounds). First the retention time deviation of these peak groups is described by fitting either a polynomial (\xe2\x80\x98smooth = "loess"\xe2\x80\x99) or a linear ( \xe2\x80\x98smooth = "linear"\xe2\x80\x99) model to the data points. These models are subsequently used to adjust the retention time of each spectrum in each sample.\n+ | See the PeakGroups_manual_\n+\n+**Obiwarp**\n+\n+ | This method performs retention time adjustment using the Obiwarp method [Prince 2006]. It is based on the code at http://obi-warp.sourceforge.net but supports alignment of multiple samples by aligning each against a _center_ sample. The alignment is performed directly on the \xe2\x80\x98profile-matrix\xe2\x80\x99 and can hence be performed independently of the peak detection or peak grouping.\n+ | See the Obiwarp_manual_\n+\n+.. _PeakGroups_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-peakGroups.html#heading-2\n+.. _Obiwarp_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-obiwarp.html\n+\n+WARNING: if a retention time ajustment have already been applied to your data.\n+The function applyAdjustedRtime will replace raw retention times with adjusted retention times and so alloww to cumulate the ajustments.\n+\n+@HELP_XCMS_MANUAL@\n+\n+------------\n+Output files\n+------------\n+\n+xset.groupChromPeaks.adjustRtime.RData: rdata.xcms.retcor format\n+\n+ | Rdata file that will be necessary in the **xcms.groupChromPeaks** step of the workflow.\n+\n+\n+---------------------------------------------------\n+\n+Changelog/News\n+--------------\n+\n+@HELP_XCMS_NEWVERSION_31200@\n+\n+**Version 3.6.1+galaxy1 - 13/02/2020**\n+\n+- NEW: if a retention time ajustment have already been applied to your data. The function applyAdjustedRtime will replace raw retention times with adjusted retention times and so alloww to cumulate the ajustments.\n+\n+@HELP_XCMS_NEWVERSION_3610@\n+\n+**Version 3.4.4.1 - 30/04/2019**\n+\n+- BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms.\n+\n+@HELP_XCMS_NEWVERSION_3440@\n+\n+**Version 3.0.0.0 - 08/03/2018**\n+\n+- 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.\n+\n+- NEW: a bunch of new options: Obiwarp.(centerSample, response, distFun, gapInit, gapExtend, factorDiag, factorGap, localAlignment, initPenalty)\n+\n+- IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values.\n+\n+- CHANGE: removing of the TIC and BPC plots. You can now use the dedicated tool "xcms plot chromatogram"\n+\n+\n+**Version 2.1.1 - 29/11/2017**\n+\n+- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C\n+\n+\n+**Version 2.1.0 - 03/02/2017**\n+\n+- IMPROVEMENT: xcms.retcor can deal with merged individual data\n+\n+\n+**Version 2.0.8 - 22/12/2016**\n+\n+- BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph\n+\n+\n+@HELP_XCMS_NEWVERSION_2090@\n+\n+\n+**Version 2.0.6 - 04/04/2016**\n+\n+- TEST: refactoring to pass planemo test using conda dependencies\n+\n+\n+**Version 2.0.5 - 10/02/2016**\n+\n+- BUGFIX: better management of errors. Datasets remained green although the process failed\n+\n+- BUGFIX: some pdf remained empty even when the process succeed\n+\n+- UPDATE: refactoring of internal management of inputs/outputs\n+\n+- UPDATE: refactoring to feed the new report tool\n+\n+\n+**Version 2.0.2 - 02/06/2015**\n+\n+- 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.\n+\n+- IMPROVEMENT: parameter labels have changed to facilitate their reading.\n+\n+\n+ ]]></help>\n+\n+\n+ <expand macro="citation" />\n+\n+</tool>\n' |
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| diff -r 36480435e92b -r 8242376d9f35 xcms_refine.r --- a/xcms_refine.r Mon Sep 11 09:21:15 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,126 +0,0 @@ -#!/usr/bin/env Rscript - -# ----- LOG FILE ----- -log_file <- file("log.txt", open = "wt") -sink(log_file) -sink(log_file, type = "output") - - -# ----- PACKAGE ----- -cat("\tSESSION INFO\n") - -#Import the different functions -source_local <- function(fname) { - argv <- commandArgs(trailingOnly = FALSE) - base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) - source(paste(base_dir, fname, sep = "/")) -} -source_local("lib.r") - -pkgs <- c("xcms", "batch", "RColorBrewer") -loadAndDisplayPackages(pkgs) -cat("\n\n") - -# ----- ARGUMENTS ----- -cat("\tARGUMENTS INFO\n") -# interpretation of arguments given in command line as an R list of objects -args <- parseCommandArgs(evaluate = FALSE) -write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t") - -cat("\n\n") - -# ----- PROCESSING INFILE ----- -cat("\tARGUMENTS PROCESSING INFO\n") - -#saving the specific parameters -args_method <- args$method -args_image <- args$image -args_msLevel <- args$msLevel -param_args <- list() - -if (args_method == "CleanPeaks") { - param_args$maxPeakwidth <- args$maxPeakwidth -} else if (args_method == "FilterIntensity") { - param_args$threshold <- args$threshold - param_args$value <- args$value - param_args$nValues <- args$nValues -} else if (args_method == "MergeNeighboringPeaks") { - param_args$expandRt <- args$expandRt - param_args$expandMz <- args$expandMz - param_args$ppm <- args$ppm - param_args$minProp <- args$minProp -} - -cat("\n\n") - - -# ----- ARGUMENTS PROCESSING ----- -cat("\tINFILE PROCESSING INFO\n") - -#image is an .RData file necessary to use xset variable given by previous tools -load(args_image) -if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. Such RData as this might have been created by an old version of XMCS 2.*") - -# Handle infiles -if (!exists("singlefile")) singlefile <- NULL -if (!exists("zipfile")) zipfile <- NULL -rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) -zipfile <- rawFilePath$zipfile -singlefile <- rawFilePath$singlefile - -cat("\n\n") - - -# ----- MAIN PROCESSING INFO ----- -cat("\tMAIN PROCESSING INFO\n") - - -cat("\t\tPREPARE PARAMETERS\n\n") - -if (args_method == "CleanPeaks") { - refineChromPeaksParam <- CleanPeaksParam(maxPeakwidth = param_args$maxPeakwidth) -} else if (args_method == "FilterIntensity") { - refineChromPeaksParam <- FilterIntensityParam( - threshold = param_args$threshold, - nValues = param_args$nValues, - value = param_args$value - ) -} else if (args_method == "MergeNeighboringPeaks") { - refineChromPeaksParam <- MergeNeighboringPeaksParam( - expandRt = param_args$expandRt, - expandMz = param_args$expandMz, - ppm = param_args$ppm, - minProp = param_args$minProp - ) -} - -cat(str(refineChromPeaksParam)) - -cat("\n\n\t\tCOMPUTE\n") - -xdata <- updateObject(xdata) - -xdata <- refineChromPeaks(xdata, param = refineChromPeaksParam) - -cat("\n\n") - -# ----- EXPORT ----- - -cat("\tXCMSnExp OBJECT INFO\n") -print(xdata) -cat("\n\n") - -cat("\txcmsSet OBJECT INFO\n") -# Get the legacy xcmsSet object -xset <- getxcmsSetObject(xdata) -print(xset) -cat("\n\n") - -#saving R data in .Rdata file to save the variables used in the present tool -objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") -save(list = objects2save[objects2save %in% ls()], file = "xcmsSet.RData") - -cat("\n\n") - - -cat("\tDONE\n") |
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| diff -r 36480435e92b -r 8242376d9f35 xcms_retcor.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xcms_retcor.r Thu Mar 14 15:35:44 2024 +0000 |
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| @@ -0,0 +1,107 @@ +#!/usr/bin/env Rscript + +# ----- LOG FILE ----- +log_file <- file("log.txt", open = "wt") +sink(log_file) +sink(log_file, type = "output") + + +# ----- PACKAGE ----- +cat("\tSESSION INFO\n") + +#Import the different functions +source_local <- function(fname) { + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep = "/")) +} +source_local("lib.r") + +pkgs <- c("xcms", "batch", "RColorBrewer") +loadAndDisplayPackages(pkgs) +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 = FALSE, quote = FALSE, sep = "\t") + +cat("\n\n") + +# ----- PROCESSING INFILE ----- +cat("\tARGUMENTS PROCESSING INFO\n") + +#saving the specific parameters +method <- args$method + +cat("\n\n") + + +# ----- ARGUMENTS PROCESSING ----- +cat("\tINFILE PROCESSING INFO\n") + +#image is an .RData file necessary to use xset variable given by previous tools +load(args$image) +args$image <- NULL +if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") + +# Handle infiles +if (!exists("singlefile")) singlefile <- NULL +if (!exists("zipfile")) zipfile <- NULL +rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) +zipfile <- rawFilePath$zipfile +singlefile <- rawFilePath$singlefile + +cat("\n\n") + + +# ----- MAIN PROCESSING INFO ----- +cat("\tMAIN PROCESSING INFO\n") + + +cat("\t\tCOMPUTE\n") + +cat("\t\t\tAlignment/Retention Time correction\n") +# clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ... +args <- args[names(args) %in% slotNames(do.call(paste0(method, "Param"), list()))] + +adjustRtimeParam <- do.call(paste0(method, "Param"), args) +print(adjustRtimeParam) + +if (hasAdjustedRtime(xdata)) { + cat("WARNING: a retention time ajustment had already been applied to your data.\nThe function applyAdjustedRtime was processed to cumulate the ajustment") + cat("Replace raw retention times with adjusted retention times.\n") + xdata <- applyAdjustedRtime(xdata) +} +xdata <- adjustRtime(xdata, param = adjustRtimeParam) + +cat("\n\n") + + +# -- TIC -- +cat("\t\tDRAW GRAPHICS\n") +getPlotAdjustedRtime(xdata) + +cat("\n\n") + +# ----- EXPORT ----- + +cat("\tXCMSnExp OBJECT INFO\n") +print(xdata) +cat("\n\n") + +cat("\txcmsSet OBJECT INFO\n") +# Get the legacy xcmsSet object +xset <- getxcmsSetObject(xdata) +print(xset) +cat("\n\n") + +#saving R data in .Rdata file to save the variables used in the present tool +objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") +save(list = objects2save[objects2save %in% ls()], file = "retcor.RData") + +cat("\n\n") + + +cat("\tDONE\n") |