Mercurial > repos > lecorguille > xcms_xcmsset

annotate README.rst @ 28:378ddb410225 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 4dc5751176d47d41fa1dec33eb443e335a1a316f
author workflow4metabolomics
date Fri, 26 Jul 2019 10:26:24 -0400
parents 3bd53dcfa438
children 14b1c52fae62
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
1 Job Dynamic Destination Mapping
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
2 -------------------------------
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
3
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
4 **Why**
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
5
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
6 xcmsSet wrapper allow both individual file and zip file which can contain several samples.
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
7 Thus, it can be interesting to adjust the number of thread according to the input type.
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
8 For example: 1 thread for a single mzXML or NetCDF file and 8 threads for a zip file.
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
9
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
10 **What**
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
11
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
12 The [Dynamic Destination Mapping](https://galaxyproject.org/admin/config/jobs/#dynamic-destination-mapping) allow Galaxy to choose a destination at runtime based on factors such as the job inputs, user submitting the job, cluster status, etc...
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
13
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
14 **How**
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
15
13
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
16 1. The file [`destinations_input_type.py`](https://raw.githubusercontent.com/workflow4metabolomics/xcms/master/galaxy/xcms_xcmsset/destinations_input_type.py) (shiped with this tool) must be place in `lib/galaxy/jobs/rules/`
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
17 2. The `job_conf.xml` must be inspired by the [`job_conf.xml.sample`](https://github.com/workflow4metabolomics/xcms/blob/master/galaxy/xcms_xcmsset/job_conf.xml.sample) shiped with this tool
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
18 3. The final destination names must match between the `job_conf.xml` and the `destinations_input_type.py`
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
19 4. Restart Galaxy
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
20
5
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
21
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
22 Changelog/News
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
23 --------------
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
24
22
1f6fb923bc4a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9
lecorguille
parents: 21
diff changeset
25 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
21
87df3692c68d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
parents: 15
diff changeset
26
27
3bd53dcfa438 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 22
diff changeset
27 **Version 3.4.4.1 - 30/04/2019**
3bd53dcfa438 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 22
diff changeset
28
3bd53dcfa438 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 22
diff changeset
29 - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms.
3bd53dcfa438 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 22
diff changeset
30
22
1f6fb923bc4a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9
lecorguille
parents: 21
diff changeset
31 **Version 3.4.4.0 - 08/02/2019**
1f6fb923bc4a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9
lecorguille
parents: 21
diff changeset
32
1f6fb923bc4a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9
lecorguille
parents: 21
diff changeset
33 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
21
87df3692c68d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
parents: 15
diff changeset
34
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
35 **Version 3.0.0.0 - 08/03/2018**
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
36
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
37 - 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.
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
38
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
39 - NEW: a bunch of new options: Spectra Filters (previously scanrange), CentWave.(mzCenterFun, fitgauss, verboseColumns), MatchedFilter.(sigma, impute, baseValue, max), MSW.(verboseColumns), ...
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
40
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
41 - UPDATE: since xcms 3.0.0, some options are no more available: scanrange (replace by filters), profmethod, MatchedFilter.step, MatchedFilter.sigma, MSW.winSize.noise, MSW.SNR.method
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
42
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
43 - IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values.
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
44
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
45 - IMPROVEMENT: the tool "should" be now more flexible in term of file naming: it "should" accept space and comma. But don't be too imaginative :)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
46
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
47 - CHANGE: removing of the TIC and BPC plots. You can new use the dedicated tool "xcms plot chromatogram"
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
48
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
49
13
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
50 **Version 2.1.1 - 29/11/2017**
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
51
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
52 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
53
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
54
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
55 **Version 2.1.0 - 22/02/2017**
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
56
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
57 - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
58
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
59 - BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
60
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
61
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
62 **Version 2.0.11 - 22/12/2016**
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
63
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
64 - BUGFIX: propose scanrange for all methods
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
65
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
66
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
67 **Version 2.0.10 - 22/12/2016**
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
68
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
69 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
70
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
71
10
69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 6
diff changeset
72 **Version 2.0.9 - 06/07/2016**
69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 6
diff changeset
73
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
74 - UPGRADE: upgrade the xcms version from 1.44.0 to 1.46.0
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
75
10
69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 6
diff changeset
76
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
77 **Version 2.0.8 - 06/04/2016**
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
78
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
79 - TEST: refactoring to pass planemo test using conda dependencies
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
80
5
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
81
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
82 **Version 2.0.7 - 10/02/2016**
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
83
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
84 - BUGFIX: better management of errors. Datasets remained green although the process failed
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
85
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
86 - BUGFIX/IMPROVEMENT: New checking steps around the imported data in order to raise explicte error message before or after launch XCMS: checking of bad characters in the filenames, checking of the XML integrity and checking of duplicates which can appear in the sample names during the XCMS process because of bad characters
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
87
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
88 - BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
89
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
90 - UPDATE: refactoring of internal management of inputs/outputs
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
91
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
92 - TEST: refactoring to feed the new report tool
5
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
93
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
94
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
95 **Version 2.0.2 - 18/01/2016**
5
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
96
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
97 - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
98
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
99
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
100 **Version 2.0.2 - 09/10/2015**
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
101
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
102 - BUGFIX: Some users reported a bug in xcms.xcmsSet. The preprocessing stops itself and doesn't import the whole dataset contained in the zip file without warning. But meanwhile, please check your samplemetadata dataset and the number of rows.
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
103
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
104
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
105 **Version 2.0.2 - 02/06/2015**
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
106
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
107 - NEW: The W4M workflows will now take as input a zip file to ease the transfer and to improve dataset exchange between tools and users. (See How_to_upload). The previous "Library directory name" is still available but we invite user to switch on the new zip system as soon as possible.
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
108
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
109 - 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.
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
110
588b0a7ae4b0 planemo upload
lecorguille
parents:
diff changeset
111 - IMPROVEMENT: parameter labels have changed to facilitate their reading.