xcms_retcor: README.rst annotate

annotate README.rst @ 22:972e76582173 draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"

author	workflow4metabolomics
date	Wed, 12 Feb 2020 08:30:30 -0500
parents	7faadba7c625
children	faf4a6b67304

rev	line source
1 da716e2937f2 planemo upload lecorguille parents: diff changeset	1
da716e2937f2 planemo upload lecorguille parents: diff changeset	2 Changelog/News
da716e2937f2 planemo upload lecorguille parents: diff changeset	3 --------------
da716e2937f2 planemo upload lecorguille parents: diff changeset	4
16 d1d78a99ba28 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9 lecorguille parents: 15 diff changeset	5 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
15 950b97b679c6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639 lecorguille parents: 10 diff changeset	6
22 972e76582173 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 21 diff changeset	7 Version 3.6.1.0 - 03/09/2019
972e76582173 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 21 diff changeset	8
972e76582173 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 21 diff changeset	9 - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
972e76582173 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 21 diff changeset	10
21 7faadba7c625 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a lecorguille parents: 16 diff changeset	11 Version 3.4.4.1 - 30/04/2019
7faadba7c625 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a lecorguille parents: 16 diff changeset	12
7faadba7c625 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a lecorguille parents: 16 diff changeset	13 - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms.
7faadba7c625 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a lecorguille parents: 16 diff changeset	14
16 d1d78a99ba28 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9 lecorguille parents: 15 diff changeset	15 Version 3.4.4.0 - 08/02/2019
d1d78a99ba28 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9 lecorguille parents: 15 diff changeset	16
d1d78a99ba28 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9 lecorguille parents: 15 diff changeset	17 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
15 950b97b679c6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639 lecorguille parents: 10 diff changeset	18
10 8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	19 Version 3.0.0.0 - 08/03/2018
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	20
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	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.
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	22
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	23 - NEW: a bunch of new options: Obiwarp.(centerSample, response, distFun, gapInit, gapExtend, factorDiag, factorGap, localAlignment, initPenalty)
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	24
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	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.
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	26
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	27 - CHANGE: removing of the TIC and BPC plots. You can new use the dedicated tool "xcms plot chromatogram"
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	28
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	29
9 e4e0254a3c0a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 8 diff changeset	30 Version 2.1.1 - 29/11/2017
e4e0254a3c0a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 8 diff changeset	31
e4e0254a3c0a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 8 diff changeset	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
e4e0254a3c0a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 8 diff changeset	33
10 8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	34
8 4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 7 diff changeset	35 Version 2.1.0 - 03/02/2017
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 7 diff changeset	36
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 7 diff changeset	37 - IMPROVEMENT: xcms.retcor can deal with merged individual data
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 7 diff changeset	38
10 8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	39
7 bb602a5b8819 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 6 diff changeset	40 Version 2.0.8 - 22/12/2016
bb602a5b8819 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 6 diff changeset	41
bb602a5b8819 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 6 diff changeset	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
bb602a5b8819 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 6 diff changeset	43
10 8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	44
6 123824c7eaa8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 2 diff changeset	45 Version 2.0.7 - 06/07/2016
123824c7eaa8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 2 diff changeset	46
123824c7eaa8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 2 diff changeset	47 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
123824c7eaa8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 2 diff changeset	48
10 8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	49
2 54cc3edfe35c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 1 diff changeset	50 Version 2.0.6 - 04/04/2016
54cc3edfe35c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 1 diff changeset	51
54cc3edfe35c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 1 diff changeset	52 - TEST: refactoring to pass planemo test using conda dependencies
54cc3edfe35c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 1 diff changeset	53
10 8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	54
1 da716e2937f2 planemo upload lecorguille parents: diff changeset	55 Version 2.0.5 - 10/02/2016
da716e2937f2 planemo upload lecorguille parents: diff changeset	56
da716e2937f2 planemo upload lecorguille parents: diff changeset	57 - BUGFIX: better management of errors. Datasets remained green although the process failed
da716e2937f2 planemo upload lecorguille parents: diff changeset	58
da716e2937f2 planemo upload lecorguille parents: diff changeset	59 - BUGFIX: some pdf remained empty even when the process succeed
da716e2937f2 planemo upload lecorguille parents: diff changeset	60
da716e2937f2 planemo upload lecorguille parents: diff changeset	61 - UPDATE: refactoring of internal management of inputs/outputs
da716e2937f2 planemo upload lecorguille parents: diff changeset	62
da716e2937f2 planemo upload lecorguille parents: diff changeset	63 - UPDATE: refactoring to feed the new report tool
da716e2937f2 planemo upload lecorguille parents: diff changeset	64
da716e2937f2 planemo upload lecorguille parents: diff changeset	65
da716e2937f2 planemo upload lecorguille parents: diff changeset	66 Version 2.0.2 - 02/06/2015
da716e2937f2 planemo upload lecorguille parents: diff changeset	67
da716e2937f2 planemo upload lecorguille parents: diff changeset	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.
da716e2937f2 planemo upload lecorguille parents: diff changeset	69
da716e2937f2 planemo upload lecorguille parents: diff changeset	70 - IMPROVEMENT: parameter labels have changed to facilitate their reading.

Mercurial > repos > lecorguille > xcms_retcor

annotate README.rst @ 22:972e76582173 draft