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date Fri, 26 Sep 2014 14:52:07 -0400
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1 # Peptide-Spectrum Match Evaluator (psm_eval) 1 GalaxyP - Peptide-Spectrum Match Evaluator
2 ==========================================
2 3
3 This repository contains the psm_eval tool that allows for 4 * Home: <https://bitbucket.org/galaxyp/psm_eval>
4 re-evaulation of identified PSM based on multiple, flexiable user 5 * Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/psm_eval>
5 supplied critiria and produces results that can be used to visualize 6 * Tool ID: `psm_eval`
6 PSMs using ProtVis
7 (https://github.com/jmchilton/protvis/tree/lorikeet-reintegration).
8 7
9 8
10 # Obtaining Tools 9 Description
10 -----------
11 11
12 Repositories for all Galaxy-P tools can be found at 12 Contains the psm_eval tool that allows for re-evaluation of identified PSM based on multiple, flexible user supplied criteria and produces results that can be used to visualize PSMs using ProtVis.
13 https:/bitbucket.org/galaxyp/.
14 13
15 # Contact 14 See:
16 15
17 Please send suggestions for improvements and bug reports to 16 * https://github.com/jmchilton/protvis/tree/lorikeet-reintegration
18 jmchilton@gmail.com. 17 * <https://bitbucket.org/Andrew_Brock/proteomics-visualise>
18 * Note, unrelated to: <http://mbostock.github.io/protovis/>
19 19
20 # License 20 System dependency note: The Python package `lxml` is used, which requires these system libraries to be installed: libxml2-devel, libxslt-devel
21 21
22 All Galaxy-P tools are licensed under the Apache License Version 2.0
23 unless otherwise documented.
24 22
25 # Tool Versioning 23 GalaxyP Community
24 -----------------
26 25
27 Galaxy-P tools will have versions of the form X.Y.Z. Versions 26 Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at:
28 differing only after the second decimal should be completely 27
29 compatible with each other. Breaking changes should result in an 28 <https://bitbucket.org/galaxyp/galaxyp>
30 increment of the number before and/or after the first decimal. All 29
31 tools of version less than 1.0.0 should be considered beta. 30
31 License
32 -------
33
34 Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below.
35
36 To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty.
37
38 You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>.
39
40 You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.
41
42
43 Contributing
44 ------------
45
46 Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out.
47
48
49 Authors
50 -------
51
52 Authors and contributors:
53
54 * Cody Wang
55 * Fred Sadler
56 * John Chilton <jmchilton@gmail.com>
57 * Minnesota Supercomputing Institute, Univeristy of Minnesota