Mercurial > repos > lecorguille > xcms_xcmsset

comparison README.rst @ 15:b62808a2a008 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author lecorguille
date Tue, 18 Sep 2018 16:07:36 -0400
parents c934dd5c49a9
children 87df3692c68d
comparison
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14:363cce459fff 15:b62808a2a008
20 20
21 21
22 Changelog/News 22 Changelog/News
23 -------------- 23 --------------
24 24
25 **Version 3.0.0.0 - 08/03/2018**
26
27 - 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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29 - NEW: a bunch of new options: Spectra Filters (previously scanrange), CentWave.(mzCenterFun, fitgauss, verboseColumns), MatchedFilter.(sigma, impute, baseValue, max), MSW.(verboseColumns), ...
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31 - UPDATE: since xcms 3.0.0, some options are no more available: scanrange (replace by filters), profmethod, MatchedFilter.step, MatchedFilter.sigma, MSW.winSize.noise, MSW.SNR.method
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33 - 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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35 - IMPROVEMENT: the tool "should" be now more flexible in term of file naming: it "should" accept space and comma. But don't be too imaginative :)
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37 - CHANGE: removing of the TIC and BPC plots. You can new use the dedicated tool "xcms plot chromatogram"
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39
25 **Version 2.1.1 - 29/11/2017** 40 **Version 2.1.1 - 29/11/2017**
26 41
27 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C 42 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
43
28 44
29 **Version 2.1.0 - 22/02/2017** 45 **Version 2.1.0 - 22/02/2017**
30 46
31 - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group". 47 - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".
32 48
33 - BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1 49 - BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1
34 50
51
35 **Version 2.0.11 - 22/12/2016** 52 **Version 2.0.11 - 22/12/2016**
36 53
37 - BUGFIX: propose scanrange for all methods 54 - BUGFIX: propose scanrange for all methods
55
38 56
39 **Version 2.0.10 - 22/12/2016** 57 **Version 2.0.10 - 22/12/2016**
40 58
41 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph 59 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
42 60
61
43 **Version 2.0.9 - 06/07/2016** 62 **Version 2.0.9 - 06/07/2016**
44 63
45 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 64 - UPGRADE: upgrade the xcms version from 1.44.0 to 1.46.0
65
46 66
47 **Version 2.0.8 - 06/04/2016** 67 **Version 2.0.8 - 06/04/2016**
48 68
49 - TEST: refactoring to pass planemo test using conda dependencies 69 - TEST: refactoring to pass planemo test using conda dependencies
50 70
57 77
58 - BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer 78 - BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer
59 79
60 - UPDATE: refactoring of internal management of inputs/outputs 80 - UPDATE: refactoring of internal management of inputs/outputs
61 81
62 - UPDATE: refactoring to feed the new report tool 82 - TEST: refactoring to feed the new report tool
63 83
64 84
65 **Version 2.0.2 - 18/01/2016** 85 **Version 2.0.2 - 18/01/2016**
66 86
67 - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases. 87 - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.