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annotate README.rst @ 25:a066b8581b97 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40"
author workflow4metabolomics
date Tue, 28 Apr 2020 09:34:27 -0400
parents 761913919c21
children d45a786cbc40
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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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9 - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
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11 **Version 3.4.4.0 - 08/02/2019**
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13 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
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15 - BUGFIX: issue with Inf values in the exported DataMatrix: https://github.com/sneumann/xcms/issues/323#issuecomment-433044378
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17 **Version 3.0.0.1 - 09/11/2018**
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19 - BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist
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21 **Version 3.0.0.0 - 08/03/2018**
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23 - 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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25 - NEW: a bunch of new options: PeakDensity.minSamples), MzClust.minSamples)
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27 - NEW: a new density plot
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29 - 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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32 **Version 2.1.1 - 29/11/2017**
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34 - 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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37 **Version 2.1.0 - 07/02/2017**
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39 - IMPROVEMENT: Add an option to export the peak list at this step without have to wait camara.annotate
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41 - IMPROVEMENT: xcms.group can deal with merged individual data from "xcms.xcmsSet Merger"
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43 - 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
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46 **Version 2.0.6 - 06/07/2016**
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48 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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51 **Version 2.0.5 - 04/04/2016**
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53 - TEST: refactoring to pass planemo test using conda dependencies
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56 **Version 2.0.4 - 10/02/2016**
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58 - BUGFIX: better management of errors. Datasets remained green although the process failed
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60 - UPDATE: refactoring of internal management of inputs/outputs
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62 - UPDATE: refactoring to feed the new report tool
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65 **Version 2.0.2 - 02/06/2015**
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67 - 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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69 - IMPROVEMENT: parameter labels have changed to facilitate their reading.