Mercurial > repos > lecorguille > xcms_group

annotate README.rst @ 16:6a4d8753a330 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty
author lecorguille
date Thu, 04 Oct 2018 10:37:03 -0400
parents 833d2c821d9c
children 7a19925478e8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
1
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
2 Changelog/News
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
3 --------------
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
4
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
5 **Version 3.0.0.0 - 08/03/2018**
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
6
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
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.
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
8
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
9 - NEW: a bunch of new options: PeakDensity.minSamples), MzClust.minSamples)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
10
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
11 - NEW: a new density plot
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
12
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
13 - IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values.
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
15
13
13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 10
diff changeset
16 **Version 2.1.1 - 29/11/2017**
13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 10
diff changeset
17
13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 10
diff changeset
18 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 10
diff changeset
19
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
20
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
21 **Version 2.1.0 - 07/02/2017**
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
22
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
23 - IMPROVEMENT: Add an option to export the peak list at this step without have to wait camara.annotate
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
24
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
25 - IMPROVEMENT: xcms.group can deal with merged individual data from "xcms.xcmsSet Merger"
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
26
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
27 - BUGFIX: the default value of "density" -> "Maximum number of groups to identify in a single m/z slice" which was of 5 have been changed to fix with the XMCS default values to 50
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
28
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
29
8
5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 4
diff changeset
30 **Version 2.0.6 - 06/07/2016**
5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 4
diff changeset
31
5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 4
diff changeset
32 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 4
diff changeset
33
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
34
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
35 **Version 2.0.5 - 04/04/2016**
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
36
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
37 - TEST: refactoring to pass planemo test using conda dependencies
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
38
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
39
3
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
40 **Version 2.0.4 - 10/02/2016**
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
41
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
42 - BUGFIX: better management of errors. Datasets remained green although the process failed
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
43
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
44 - UPDATE: refactoring of internal management of inputs/outputs
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
45
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
46 - UPDATE: refactoring to feed the new report tool
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
47
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
48
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
49 **Version 2.0.2 - 02/06/2015**
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
50
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
51 - 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.
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
52
98e33cdf0eb1 planemo upload
lecorguille
parents:
diff changeset
53 - IMPROVEMENT: parameter labels have changed to facilitate their reading.