Mercurial > repos > lecorguille > xcms_retcor

annotate README.rst @ 48:366ff564f949 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 dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author workflow4metabolomics
date Wed, 07 Apr 2021 10:31:56 +0000
parents 32c1cbdbdd3b
children
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
48
366ff564f949 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 46
diff changeset
7 **Version 3.12.0+galaxy* - 03/03/2020**
366ff564f949 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 46
diff changeset
8
366ff564f949 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 46
diff changeset
9 - UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_)
366ff564f949 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 46
diff changeset
10
46
32c1cbdbdd3b "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"
workflow4metabolomics
parents: 45
diff changeset
11 **Version 3.6.1+galaxy1 - 13/02/2020**
32c1cbdbdd3b "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"
workflow4metabolomics
parents: 45
diff changeset
12
32c1cbdbdd3b "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"
workflow4metabolomics
parents: 45
diff changeset
13 - 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.
32c1cbdbdd3b "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"
workflow4metabolomics
parents: 45
diff changeset
14
45
1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 44
diff changeset
15 **Version 3.6.1.0 - 03/09/2019**
1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 44
diff changeset
16
1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 44
diff changeset
17 - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
1986c48d86ce "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 44
diff changeset
18
44
db348cb32618 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 43
diff changeset
19 **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
20
db348cb32618 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 43
diff changeset
21 - 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
22
43
221a8c6de94a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
lecorguille
parents: 42
diff changeset
23 **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
24
221a8c6de94a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
lecorguille
parents: 42
diff changeset
25 - 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
26
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
27 **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
28
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
29 - 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
30
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
31 - 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
32
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
33 - 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
34
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
35 - 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
36
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
37
29
c013ed353a2f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents: 27
diff changeset
38 **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
39
29
c013ed353a2f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents: 27
diff changeset
40 - 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
41
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
42
16
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 14
diff changeset
43 **Version 2.1.0 - 03/02/2017**
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 14
diff changeset
44
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 14
diff changeset
45 - 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
46
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
47
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
48 **Version 2.0.8 - 22/12/2016**
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
49
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 12
diff changeset
50 - 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
51
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
52
12
aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 8
diff changeset
53 **Version 2.0.7 - 06/07/2016**
aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 8
diff changeset
54
aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 8
diff changeset
55 - 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
56
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
57
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
58 **Version 2.0.6 - 04/04/2016**
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
59
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
60 - TEST: refactoring to pass planemo test using conda dependencies
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
61
33
69b5a006fca1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 29
diff changeset
62
5
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
63 **Version 2.0.5 - 10/02/2016**
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
64
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
65 - BUGFIX: better management of errors. Datasets remained green although the process failed
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
66
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
67 - BUGFIX: some pdf remained empty even when the process succeed
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
68
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
69 - UPDATE: refactoring of internal management of inputs/outputs
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
70
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
71 - UPDATE: refactoring to feed the new report tool
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
72
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
73
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
74 **Version 2.0.2 - 02/06/2015**
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
75
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
76 - 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
77
d0efb2c07577 planemo upload
lecorguille
parents:
diff changeset
78 - IMPROVEMENT: parameter labels have changed to facilitate their reading.