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comparison README.rst @ 3:b800001c9f30 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
author computational-metabolomics
date Thu, 09 Apr 2020 14:30:41 -0400
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2:d4376a743f7b 3:b800001c9f30
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