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Repository xcms_group

Name: xcms_group

Owner: lecorguille

Synopsis: [Metabolomics][W4M][LC-MS] XCMS R Package - Preprocessing - Group peaks from different samples together

Detailed description:

Group peaks together across samples using overlapping m/z bins and
calculation of smoothed peak distributions in chromatographic time.
Part of the W4M project: http://workflow4metabolomics.org
XCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html

Content homepage: https://github.com/sneumann/xcms

Development repository: https://github.com/workflow4metabolomics/tools-metabolomics/

Link to this repository revision: https://toolshed.g2.bx.psu.edu/view/lecorguille/xcms_group/d45a786cbc40

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group

Type: unrestricted

Revision: 27:d45a786cbc40

This revision can be installed: True

Times cloned / installed: 1549

Repository README files - may contain important installation or license information

Readme files

Changelog/News -------------- .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS **Version 3.12.0+galaxy* - 03/03/2020** - UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_) **Version 3.6.1.0 - 03/09/2019** - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_) **Version 3.4.4.0 - 08/02/2019** - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) - BUGFIX: issue with Inf values in the exported DataMatrix: https://github.com/sneumann/xcms/issues/323#issuecomment-433044378 **Version 3.0.0.1 - 09/11/2018** - BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist **Version 3.0.0.0 - 08/03/2018** - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed. - NEW: a bunch of new options: PeakDensity.minSamples), MzClust.minSamples) - NEW: a new density plot - IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values. **Version 2.1.1 - 29/11/2017** - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C **Version 2.1.0 - 07/02/2017** - IMPROVEMENT: Add an option to export the peak list at this step without have to wait camara.annotate - IMPROVEMENT: xcms.group can deal with merged individual data from "xcms.xcmsSet Merger" - BUGFIX: the default value of "density" -> "Maximum number of groups to identify in a single m/z slice" which was of 5 have been changed to fix with the XMCS default values to 50 **Version 2.0.6 - 06/07/2016** - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 **Version 2.0.5 - 04/04/2016** - TEST: refactoring to pass planemo test using conda dependencies **Version 2.0.4 - 10/02/2016** - BUGFIX: better management of errors. Datasets remained green although the process failed - UPDATE: refactoring of internal management of inputs/outputs - UPDATE: refactoring to feed the new report tool **Version 2.0.2 - 02/06/2015** - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors. - IMPROVEMENT: parameter labels have changed to facilitate their reading.