xcms_fillpeaks: README.rst annotate

annotate README.rst @ 14:d78d3d4a82db draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857

author	lecorguille
date	Wed, 19 Sep 2018 02:55:17 -0400
parents	91c71f3808f3
children	34fe699200ce

rev	line source
3 5a54397dbc97 planemo upload lecorguille parents: diff changeset	1
5a54397dbc97 planemo upload lecorguille parents: diff changeset	2 Changelog/News
5a54397dbc97 planemo upload lecorguille parents: diff changeset	3 --------------
5a54397dbc97 planemo upload lecorguille parents: diff changeset	4
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 12 diff changeset	5 Version 3.0.0.0 - 08/03/2018
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 12 diff changeset	6
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 12 diff changeset	7 - 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.
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 12 diff changeset	8
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 12 diff changeset	9 - UPDATE: since xcms 3.0.0, the selection of a method is no more needed (chrom or MSW). xcms will detect from the data the peak picking method used in findChromPeaks
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 12 diff changeset	10
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 12 diff changeset	11 - UPDATE: since xcms 3.0.0, new parameters are available: expandMz, expandRt and ppm
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 12 diff changeset	12
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 12 diff changeset	13
12 dcb9041cb9ea planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 11 diff changeset	14 Version 2.1.1 - 29/11/2017
dcb9041cb9ea planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 11 diff changeset	15
dcb9041cb9ea planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 11 diff changeset	16 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
dcb9041cb9ea planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 11 diff changeset	17
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 12 diff changeset	18
11 de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	19 Version 2.1.0 - 07/02/2017
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	20
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	21 - IMPROVEMENT: change the management of the peaklist ids. The main ids remain the same as xcms generated. The export setiings now only add custom names in the variableMetadata tab (namecustom)
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	22
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	23 - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data
de0d85537ee3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 9 diff changeset	24
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 12 diff changeset	25
9 ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 8 diff changeset	26 Version 2.0.8 - 22/12/2016
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 8 diff changeset	27
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 12 diff changeset	28 - IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate
91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 12 diff changeset	29
9 ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 8 diff changeset	30
8 cce30b3398e0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 4 diff changeset	31 Version 2.0.7 - 06/07/2016
cce30b3398e0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 4 diff changeset	32
cce30b3398e0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 4 diff changeset	33 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
cce30b3398e0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 4 diff changeset	34
13 91c71f3808f3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 12 diff changeset	35
4 2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	36 Version 2.0.6 - 04/04/2016
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	37
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	38 - TEST: refactoring to pass planemo test using conda dependencies
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	39
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	40
3 5a54397dbc97 planemo upload lecorguille parents: diff changeset	41 Version 2.0.5 - 10/02/2016
5a54397dbc97 planemo upload lecorguille parents: diff changeset	42
5a54397dbc97 planemo upload lecorguille parents: diff changeset	43 - BUGFIX: better management of errors. Datasets remained green although the process failed
5a54397dbc97 planemo upload lecorguille parents: diff changeset	44
5a54397dbc97 planemo upload lecorguille parents: diff changeset	45 - UPDATE: refactoring of internal management of inputs/outputs
5a54397dbc97 planemo upload lecorguille parents: diff changeset	46
5a54397dbc97 planemo upload lecorguille parents: diff changeset	47 - UPDATE: refactoring to feed the new report tool
5a54397dbc97 planemo upload lecorguille parents: diff changeset	48
5a54397dbc97 planemo upload lecorguille parents: diff changeset	49
5a54397dbc97 planemo upload lecorguille parents: diff changeset	50 Version 2.0.2 - 02/06/2015
5a54397dbc97 planemo upload lecorguille parents: diff changeset	51
5a54397dbc97 planemo upload lecorguille parents: diff changeset	52 - 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.
5a54397dbc97 planemo upload lecorguille parents: diff changeset	53
5a54397dbc97 planemo upload lecorguille parents: diff changeset	54 - IMPROVEMENT: parameter labels have changed to facilitate their reading.

Mercurial > repos > lecorguille > xcms_fillpeaks

annotate README.rst @ 14:d78d3d4a82db draft