diff README.rst @ 15:b62808a2a008 draft

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
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--- a/README.rst	Tue Feb 13 04:47:50 2018 -0500
+++ b/README.rst	Tue Sep 18 16:07:36 2018 -0400
@@ -22,27 +22,47 @@
 Changelog/News
 --------------
 
+**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: Spectra Filters (previously scanrange), CentWave.(mzCenterFun, fitgauss, verboseColumns), MatchedFilter.(sigma, impute, baseValue, max), MSW.(verboseColumns), ...
+
+- 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
+
+- IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values.
+
+- 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 :)
+
+- CHANGE: removing of the TIC and BPC plots. You can new use the dedicated tool "xcms plot chromatogram"
+
+
 **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 - 22/02/2017**
 
 - 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".
 
 - 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
 
+
 **Version 2.0.11 - 22/12/2016**
 
 - BUGFIX: propose scanrange for all methods
 
+
 **Version 2.0.10 - 22/12/2016**
 
 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
 
+
 **Version 2.0.9 - 06/07/2016**
 
-- UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
+- UPGRADE: upgrade the xcms version from 1.44.0 to 1.46.0
+
 
 **Version 2.0.8 - 06/04/2016**
 
@@ -59,7 +79,7 @@
 
 - UPDATE: refactoring of internal management of inputs/outputs
 
-- UPDATE: refactoring to feed the new report tool
+- TEST: refactoring to feed the new report tool
 
 
 **Version 2.0.2 - 18/01/2016**