Mercurial > repos > computational-metabolomics > mspurity_dimspredictpuritysingle
comparison README.rst @ 3:8f5877c6d5f4 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
author | computational-metabolomics |
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date | Thu, 09 Apr 2020 14:24:53 -0400 |
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children | 84d4e78d49f2 |
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1 msPurity for Galaxy | |
2 ======================== | |
3 |Build Status (Travis)| |Git| |Bioconda| |License| | |
4 | |
5 | |
6 Version v1.12.2+galaxy1 | |
7 ------ | |
8 | |
9 - msPurity | |
10 - bioconductor-mspurity v1.12.2 | |
11 - Galaxy tools | |
12 - v1 | |
13 | |
14 About | |
15 ------ | |
16 Galaxy tools for the Bioconductor R package msPurity. Tools available for assessing precursor ion purity of | |
17 LC-MS/MS or DI-M/MS data that has been acquired. And tools are available to assess LC-MS or DI-MS for | |
18 anticipated precursor ion purity to guide a later fragmentation experiment. | |
19 | |
20 Additional, tools available to perform LC-MS/MS spectral matching. | |
21 | |
22 Associated paper `msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics. Analytical Chemistry <http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b04358>`_ | |
23 | |
24 Use the following links for more details of the msPurity R package: | |
25 | |
26 * Bioconductor: http://bioconductor.org/packages/msPurity/ | |
27 * Vignette: https://bioconductor.org/packages/devel/bioc/vignettes/msPurity/inst/doc/msPurity-vignette.html | |
28 * Manual: http://bioconductor.org/packages/devel/bioc/manuals/msPurity/man/msPurity.pdf | |
29 * Bioconductor mirror code: https://github.com/Bioconductor-mirror/msPurity | |
30 * Github code: https://github.com/computational-metabolomics/mspurity | |
31 * Bioconda (stable): https://anaconda.org/bioconda/bioconductor-mspurity | |
32 * Conda (dev and testing): https://anaconda.org/tomnl/bioconductor-mspurity | |
33 | |
34 | |
35 | |
36 | |
37 Dependencies | |
38 ------ | |
39 Dependencies for these Galaxy tools should be handled by CONDA. The most recent version of the msPurity R package can found on channel `tomnl <https://anaconda.org/tomnl/bioconductor-mspurity>`_ on `anaconda <https://anaconda.org/tomnl/bioconductor-mspurity>`_. Warning this will be a different version of the package compared to the BICONDA bioconductor-mspurity. | |
40 | |
41 | |
42 Galaxy | |
43 ------ | |
44 `Galaxy <https://galaxyproject.org>`_ is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. | |
45 | |
46 | |
47 Authors, contributors & contacts | |
48 ------------------------- | |
49 | |
50 - Thomas N. Lawson (t.n.lawson@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_ | |
51 - Ralf J. M. Weber (r.j.weber@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_ | |
52 - Jordi Capellades (j.capellades.to@gmail.com) - `Universitat Rovira i Virgili (SP) <http://www.urv.cat/en/>`_ | |
53 - Julien Saint-Vanne (jsaintvanne) - `ABiMS (France) <http://abims.sb-roscoff.fr/>`_ | |
54 - Simon Bray (sbray@informatik.uni-freiburg.de) - `University of Freiburg (Germany) <https://www.uni-freiburg.de/>`_ | |
55 | |
56 Changes | |
57 ------------------------- | |
58 v1.12.2-galaxy1 | |
59 - grpPeaklist reference incorrect in createDatabase.xml | |
60 - Add custom adduct handling for createMSP | |
61 - Change output of flagRemove to tabular | |
62 | |
63 | |
64 v1.12.2-galaxy0 | |
65 - Update to version v1.12.2 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_ | |
66 - Optional summary output for combineAnnotations (for very large output) | |
67 - Extra column added to flagRemove output | |
68 - Hide probmetab input | |
69 - Make dimsPredictPuritySingle more compatible with "simple workflow inputs" | |
70 | |
71 | |
72 v1.12.1-galaxy0 | |
73 - Update to version v1.12.1 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_ | |
74 | |
75 v1.12.0-galaxy1 | |
76 - Bug fix (offsets were not being automatically selected for purityA) thanks jsaintvanne | |
77 - Exit script without error for flagRemove | |
78 - Username updated in Toolshed yaml | |
79 | |
80 v1.12.0-galaxy0 | |
81 - Updates for Bioconductor stable msPurity v1.12.0 release | |
82 - Additional columns added for spectral matching (for msnpy use case) | |
83 - Merge of v1.11.4-galaxy1 | |
84 | |
85 v1.11.4-galaxy1 | |
86 - Not submitted to toolshed | |
87 - Update to follow IUC guidelines for Galaxy tool development | |
88 | |
89 v1.11.4-galaxy0.2.7 | |
90 - submitted to test toolshed (20190927) | |
91 - Bug fix for spectralMatching choice of instrument types | |
92 | |
93 v1.11.4-galaxy0.2.6: | |
94 - submitted to test toolshed (20190924) | |
95 - Bug fix for createAnnotation database local path | |
96 - Update of instrument types for spectral matching | |
97 - Update of split_msp tool to handle different MSP types | |
98 | |
99 | |
100 v1.11.4-galaxy0.2.5: | |
101 - submitted to test toolshed (20190913) | |
102 - Added ppmInterp parameter to purityA | |
103 - Complete update of combineAnnotation tool to use either sqlite, postgres or mysql database | |
104 - Update of spectralMatching tool to use either sqlite, postgres or mysql database | |
105 - Added include_adducts parameter to createMSP | |
106 | |
107 v1.11.3-galaxy0.2.5: | |
108 - Note: This was not pushed to test toolshed | |
109 - Clean up of the versioning to be in line with IUC | |
110 - All tools updated with the same versioning | |
111 - Bump to msPurity v1.11.3 to so EIC is calculated for all features | |
112 | |
113 v0.2.5 (spectralMatching): | |
114 - spectralMatching - Extra details from matched library spectra is now added to the database (fix) | |
115 | |
116 v0.2.4 (all tools): | |
117 - bioconductor-mspurity v1.11.2 now used. Fixes EIC problems for MS/MS data | |
118 | |
119 v0.2.2 (spectralMatching): | |
120 - spectralMatching - Extra details from matched library spectra is now added to the database | |
121 | |
122 v0.2.3 (createDatabase): | |
123 - createDatabase.xml fix for EIC creation | |
124 | |
125 v0.2.2 (createDatabase, flagRemove, combineAnnotation): | |
126 - createDatabase.xml fix for xcms3 and CAMERA | |
127 - flagRemove xcms3 fix | |
128 - combineAnnotation Made sirius, probmetab and metfrag optional | |
129 - combineAnnotation fix column sirius | |
130 | |
131 v0.2.1 (all tools): | |
132 - Update msPurity R code version (bug fix for createMSP and xcms3 version check for createDatabase) | |
133 | |
134 v0.2.0 (all tools): | |
135 - Update all tools to be more consistent with msPurity core code | |
136 | |
137 License | |
138 ------- | |
139 Released under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/LICENSE>`_) | |
140 | |
141 | |
142 .. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/mspurity-galaxy.svg?style=flat&maxAge=3600&label=Travis-CI | |
143 :target: https://travis-ci.org/computational-metabolomics/mspurity-galaxy | |
144 | |
145 .. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600 | |
146 :target: https://github.com/computational-metabolomics/mspurity-galaxy | |
147 | |
148 .. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600 | |
149 :target: http://bioconda.github.io/recipes/bioconductor-mspurity/README.html | |
150 | |
151 .. |License| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg | |
152 :target: https://www.gnu.org/licenses/gpl-3.0.html | |
153 | |
154 |