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Repository xcms_fillpeaks
Owner: lecorguille
Synopsis: [Metabolomics][W4M][LC-MS] XCMS R Package - Preprocessing - Integrate areas of missing peaks
For each sample, identify peak groups where that sample is not represented.
For each of those peak groups, integrate the signal in the region of that peak group and create a new peak.
Part of the W4M project: http://workflow4metabolomics.org
XCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html 
Type: unrestricted
Revision: 25:26d77e9ceb49
This revision can be installed: True
Times cloned / installed: 1163

Repository README files - may contain important installation or license information

Changelog/News -------------- .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS **Version 3.12.0+galaxy* - 03/03/2020** - UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_) **Version 3.6.1.0 - 03/09/2019** - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_) **Version 3.4.4.0 - 08/02/2019** - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) - BUGFIX: issue with Inf values in the exported DataMatrix: https://github.com/sneumann/xcms/issues/323#issuecomment-433044378 **Version 3.0.0.2 - 09/11/2018** - BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist **Version 3.0.0.1 - 09/10/2018** - IMPROVEMENT: the export of the PeakList is now mandatory **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. - UPDATE: since xcms 3.0.0, the selection of a method is no more needed (chrom or MSW). xcms will detect from the data the peak picking method used in findChromPeaks - UPDATE: since xcms 3.0.0, new parameters are available: expandMz, expandRt and ppm **Version 2.1.1 - 29/11/2017** - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C **Version 2.1.0 - 07/02/2017** - IMPROVEMENT: change the management of the peaklist ids. The main ids remain the same as xcms generated. The export setiings now only add custom names in the variableMetadata tab (namecustom) - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data **Version 2.0.8 - 22/12/2016** - IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate **Version 2.0.7 - 06/07/2016** - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 **Version 2.0.6 - 04/04/2016** - TEST: refactoring to pass planemo test using conda dependencies **Version 2.0.5 - 10/02/2016** - BUGFIX: better management of errors. Datasets remained green although the process failed - UPDATE: refactoring of internal management of inputs/outputs - UPDATE: refactoring to feed the new report tool **Version 2.0.2 - 02/06/2015** - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors. - IMPROVEMENT: parameter labels have changed to facilitate their reading.
Dependencies of this repository

Repository no_unzip_datatype revision 7800ba9a4c1e owned by lecorguille
Repository rdata_xcms_datatypes revision 544f6d2329ac owned by lecorguille

Contents of this repository

Name Description Version Minimum Galaxy Version
Integrate areas of missing peaks 3.12.0+galaxy0 16.01

Categories
Metabolomics - Tools for use in the study of Metabolomics