xcms_retcor: README.rst annotate

annotate README.rst @ 23:faf4a6b67304 draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"

author	workflow4metabolomics
date	Thu, 13 Feb 2020 06:43:08 -0500
parents	972e76582173
children	aa252eec9229

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
23 faf4a6b67304 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289" workflow4metabolomics parents: 22 diff changeset	7 Version 3.6.1+galaxy1 - 13/02/2020
faf4a6b67304 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289" workflow4metabolomics parents: 22 diff changeset	8
faf4a6b67304 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289" workflow4metabolomics parents: 22 diff changeset	9 - NEW: if a retention time ajustment have already been applied to your data. The function applyAdjustedRtime will replace raw retention times with adjusted retention times and so alloww to cumulate the ajustments.
faf4a6b67304 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289" workflow4metabolomics parents: 22 diff changeset	10
22 972e76582173 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 21 diff changeset	11 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	12
972e76582173 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 21 diff changeset	13 - 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	14
21 7faadba7c625 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a lecorguille parents: 16 diff changeset	15 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	16
7faadba7c625 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a lecorguille parents: 16 diff changeset	17 - 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	18
16 d1d78a99ba28 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9 lecorguille parents: 15 diff changeset	19 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	20
d1d78a99ba28 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9 lecorguille parents: 15 diff changeset	21 - 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	22
10 8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	23 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	24
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	25 - 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	26
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	27 - 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	28
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	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.
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	30
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	31 - 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	32
8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	33
9 e4e0254a3c0a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 8 diff changeset	34 Version 2.1.1 - 29/11/2017
e4e0254a3c0a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 8 diff changeset	35
e4e0254a3c0a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 8 diff changeset	36 - 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	37
10 8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	38
8 4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 7 diff changeset	39 Version 2.1.0 - 03/02/2017
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 7 diff changeset	40
4bfef820569b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 7 diff changeset	41 - 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	42
10 8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	43
7 bb602a5b8819 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 6 diff changeset	44 Version 2.0.8 - 22/12/2016
bb602a5b8819 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 6 diff changeset	45
bb602a5b8819 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 6 diff changeset	46 - 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	47
10 8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	48
6 123824c7eaa8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 2 diff changeset	49 Version 2.0.7 - 06/07/2016
123824c7eaa8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 2 diff changeset	50
123824c7eaa8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 2 diff changeset	51 - 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	52
10 8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	53
2 54cc3edfe35c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 1 diff changeset	54 Version 2.0.6 - 04/04/2016
54cc3edfe35c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 1 diff changeset	55
54cc3edfe35c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 1 diff changeset	56 - 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	57
10 8828cba9aedd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 9 diff changeset	58
1 da716e2937f2 planemo upload lecorguille parents: diff changeset	59 Version 2.0.5 - 10/02/2016
da716e2937f2 planemo upload lecorguille parents: diff changeset	60
da716e2937f2 planemo upload lecorguille parents: diff changeset	61 - BUGFIX: better management of errors. Datasets remained green although the process failed
da716e2937f2 planemo upload lecorguille parents: diff changeset	62
da716e2937f2 planemo upload lecorguille parents: diff changeset	63 - BUGFIX: some pdf remained empty even when the process succeed
da716e2937f2 planemo upload lecorguille parents: diff changeset	64
da716e2937f2 planemo upload lecorguille parents: diff changeset	65 - UPDATE: refactoring of internal management of inputs/outputs
da716e2937f2 planemo upload lecorguille parents: diff changeset	66
da716e2937f2 planemo upload lecorguille parents: diff changeset	67 - UPDATE: refactoring to feed the new report tool
da716e2937f2 planemo upload lecorguille parents: diff changeset	68
da716e2937f2 planemo upload lecorguille parents: diff changeset	69
da716e2937f2 planemo upload lecorguille parents: diff changeset	70 Version 2.0.2 - 02/06/2015
da716e2937f2 planemo upload lecorguille parents: diff changeset	71
da716e2937f2 planemo upload lecorguille parents: diff changeset	72 - 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	73
da716e2937f2 planemo upload lecorguille parents: diff changeset	74 - IMPROVEMENT: parameter labels have changed to facilitate their reading.

Mercurial > repos > lecorguille > xcms_retcor

annotate README.rst @ 23:faf4a6b67304 draft