Mercurial > repos > lecorguille > xcms_retcor

annotate README.rst @ 45:1986c48d86ce draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
author workflow4metabolomics
date Wed, 12 Feb 2020 13:26:47 +0000
parents db348cb32618
children 32c1cbdbdd3b
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2 Changelog/News
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3 --------------
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5 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
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7 **Version 3.6.1.0 - 03/09/2019**
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1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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9 - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
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11 **Version 3.4.4.1 - 30/04/2019**
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13 - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms.
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15 **Version 3.4.4.0 - 08/02/2019**
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17 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
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19 **Version 3.0.0.0 - 08/03/2018**
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21 - 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.
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23 - NEW: a bunch of new options: Obiwarp.(centerSample, response, distFun, gapInit, gapExtend, factorDiag, factorGap, localAlignment, initPenalty)
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25 - IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values.
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27 - CHANGE: removing of the TIC and BPC plots. You can new use the dedicated tool "xcms plot chromatogram"
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30 **Version 2.1.1 - 29/11/2017**
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32 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
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35 **Version 2.1.0 - 03/02/2017**
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37 - IMPROVEMENT: xcms.retcor can deal with merged individual data
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40 **Version 2.0.8 - 22/12/2016**
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42 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
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45 **Version 2.0.7 - 06/07/2016**
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47 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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50 **Version 2.0.6 - 04/04/2016**
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52 - TEST: refactoring to pass planemo test using conda dependencies
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55 **Version 2.0.5 - 10/02/2016**
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57 - BUGFIX: better management of errors. Datasets remained green although the process failed
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59 - BUGFIX: some pdf remained empty even when the process succeed
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61 - UPDATE: refactoring of internal management of inputs/outputs
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63 - UPDATE: refactoring to feed the new report tool
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66 **Version 2.0.2 - 02/06/2015**
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68 - 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.
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70 - IMPROVEMENT: parameter labels have changed to facilitate their reading.