Mercurial > repos > lecorguille > xcms_retcor

annotate README.rst @ 44:db348cb32618 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 60ad498b7bd01542a69d6603160d36494c97077a
author lecorguille
date Tue, 30 Apr 2019 05:19:53 -0400
parents 221a8c6de94a
children 1986c48d86ce
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
1
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
2 Changelog/News
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
3 --------------
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
4
43
221a8c6de94a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
lecorguille
parents: 42
diff changeset
5 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
42
feb216e6aef7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
parents: 33
diff changeset
6
44
db348cb32618 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 43
diff changeset
7 **Version 3.4.4.1 - 30/04/2019**
db348cb32618 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 43
diff changeset
8
db348cb32618 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 43
diff changeset
9 - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms.
db348cb32618 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 43
diff changeset
10
43
221a8c6de94a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
lecorguille
parents: 42
diff changeset
11 **Version 3.4.4.0 - 08/02/2019**
221a8c6de94a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
lecorguille
parents: 42
diff changeset
12
221a8c6de94a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
lecorguille
parents: 42
diff changeset
13 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
42
feb216e6aef7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
parents: 33
diff changeset
14
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
15 **Version 3.0.0.0 - 08/03/2018**
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
16
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
17 - 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.
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
18
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
19 - NEW: a bunch of new options: Obiwarp.(centerSample, response, distFun, gapInit, gapExtend, factorDiag, factorGap, localAlignment, initPenalty)
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
20
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
21 - IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values.
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
22
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
23 - CHANGE: removing of the TIC and BPC plots. You can new use the dedicated tool "xcms plot chromatogram"
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
24
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
25
29
c013ed353a2f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents: 27
diff changeset
26 **Version 2.1.1 - 29/11/2017**
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 16
diff changeset
27
29
c013ed353a2f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents: 27
diff changeset
28 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
27
30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 16
diff changeset
29
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
30
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 14
diff changeset
31 **Version 2.1.0 - 03/02/2017**
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 14
diff changeset
32
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 14
diff changeset
33 - IMPROVEMENT: xcms.retcor can deal with merged individual data
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 14
diff changeset
34
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
35
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
36 **Version 2.0.8 - 22/12/2016**
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
37
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
38 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
39
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
40
12
aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 8
diff changeset
41 **Version 2.0.7 - 06/07/2016**
aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 8
diff changeset
42
aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 8
diff changeset
43 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 8
diff changeset
44
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
45
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
46 **Version 2.0.6 - 04/04/2016**
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
47
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
48 - TEST: refactoring to pass planemo test using conda dependencies
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
49
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
50
5
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
51 **Version 2.0.5 - 10/02/2016**
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
52
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
53 - BUGFIX: better management of errors. Datasets remained green although the process failed
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
54
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
55 - BUGFIX: some pdf remained empty even when the process succeed
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
56
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
57 - UPDATE: refactoring of internal management of inputs/outputs
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
58
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
59 - UPDATE: refactoring to feed the new report tool
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
60
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
61
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
62 **Version 2.0.2 - 02/06/2015**
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
63
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
64 - 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.
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
65
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
66 - IMPROVEMENT: parameter labels have changed to facilitate their reading.