annotate readme.rst @ 6:ee4be6eadd34 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit ca2d37289d712b69ac15611bbf4961d083991bba
author bgruening
date Fri, 10 Nov 2017 13:04:44 -0500
parents 652f9d550531
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
652f9d550531 Uploaded
bgruening
parents:
diff changeset
1 ================================================
652f9d550531 Uploaded
bgruening
parents:
diff changeset
2 Galaxy wrapper for Infernal prediction tools
652f9d550531 Uploaded
bgruening
parents:
diff changeset
3 ================================================
652f9d550531 Uploaded
bgruening
parents:
diff changeset
4
652f9d550531 Uploaded
bgruening
parents:
diff changeset
5 Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases
652f9d550531 Uploaded
bgruening
parents:
diff changeset
6 for RNA structure and sequence similarities. It is an implementation of a special
652f9d550531 Uploaded
bgruening
parents:
diff changeset
7 case of profile stochastic context-free grammars called covariance models (CMs).
652f9d550531 Uploaded
bgruening
parents:
diff changeset
8 A CM is like a sequence profile, but it scores a combination of sequence consensus
652f9d550531 Uploaded
bgruening
parents:
diff changeset
9 and RNA secondary structure consensus, so in many cases, it is more capable of
652f9d550531 Uploaded
bgruening
parents:
diff changeset
10 identifying RNA homologs that conserve their secondary structure more than their
652f9d550531 Uploaded
bgruening
parents:
diff changeset
11 primary sequence.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
12
652f9d550531 Uploaded
bgruening
parents:
diff changeset
13 This wrapper is copyright 2013 by:
652f9d550531 Uploaded
bgruening
parents:
diff changeset
14 * Bjoern Gruening
652f9d550531 Uploaded
bgruening
parents:
diff changeset
15
652f9d550531 Uploaded
bgruening
parents:
diff changeset
16
652f9d550531 Uploaded
bgruening
parents:
diff changeset
17 This prepository contains wrapper for the Infernal_ command line tool.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
18
652f9d550531 Uploaded
bgruening
parents:
diff changeset
19 .. _Infernal: http://infernal.janelia.org/
652f9d550531 Uploaded
bgruening
parents:
diff changeset
20
652f9d550531 Uploaded
bgruening
parents:
diff changeset
21
652f9d550531 Uploaded
bgruening
parents:
diff changeset
22 The recommended citation for using Infernal 1.1 is E. P. Nawrocki and S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches , Bioinformatics 29:2933-2935 (2013).
652f9d550531 Uploaded
bgruening
parents:
diff changeset
23
652f9d550531 Uploaded
bgruening
parents:
diff changeset
24
652f9d550531 Uploaded
bgruening
parents:
diff changeset
25 ============
652f9d550531 Uploaded
bgruening
parents:
diff changeset
26 Installation
652f9d550531 Uploaded
bgruening
parents:
diff changeset
27 ============
652f9d550531 Uploaded
bgruening
parents:
diff changeset
28
652f9d550531 Uploaded
bgruening
parents:
diff changeset
29 Please install Infernal and the tool wrappers with the Galaxy Tool Shed from
652f9d550531 Uploaded
bgruening
parents:
diff changeset
30
652f9d550531 Uploaded
bgruening
parents:
diff changeset
31 http://toolshed.g2.bx.psu.edu/view/bgruening/infernal
652f9d550531 Uploaded
bgruening
parents:
diff changeset
32
652f9d550531 Uploaded
bgruening
parents:
diff changeset
33
652f9d550531 Uploaded
bgruening
parents:
diff changeset
34 =======
652f9d550531 Uploaded
bgruening
parents:
diff changeset
35 History
652f9d550531 Uploaded
bgruening
parents:
diff changeset
36 =======
652f9d550531 Uploaded
bgruening
parents:
diff changeset
37
652f9d550531 Uploaded
bgruening
parents:
diff changeset
38 - v1.1.0: Initial public release
652f9d550531 Uploaded
bgruening
parents:
diff changeset
39
652f9d550531 Uploaded
bgruening
parents:
diff changeset
40
652f9d550531 Uploaded
bgruening
parents:
diff changeset
41 Bug Reports
652f9d550531 Uploaded
bgruening
parents:
diff changeset
42 ===========
652f9d550531 Uploaded
bgruening
parents:
diff changeset
43
652f9d550531 Uploaded
bgruening
parents:
diff changeset
44 You can file an issue here https://github.com/bgruening/galaxytools/issues or ask
652f9d550531 Uploaded
bgruening
parents:
diff changeset
45 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
652f9d550531 Uploaded
bgruening
parents:
diff changeset
46
652f9d550531 Uploaded
bgruening
parents:
diff changeset
47
652f9d550531 Uploaded
bgruening
parents:
diff changeset
48 Licence (MIT)
652f9d550531 Uploaded
bgruening
parents:
diff changeset
49 =============
652f9d550531 Uploaded
bgruening
parents:
diff changeset
50
652f9d550531 Uploaded
bgruening
parents:
diff changeset
51 Permission is hereby granted, free of charge, to any person obtaining a copy
652f9d550531 Uploaded
bgruening
parents:
diff changeset
52 of this software and associated documentation files (the "Software"), to deal
652f9d550531 Uploaded
bgruening
parents:
diff changeset
53 in the Software without restriction, including without limitation the rights
652f9d550531 Uploaded
bgruening
parents:
diff changeset
54 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
652f9d550531 Uploaded
bgruening
parents:
diff changeset
55 copies of the Software, and to permit persons to whom the Software is
652f9d550531 Uploaded
bgruening
parents:
diff changeset
56 furnished to do so, subject to the following conditions:
652f9d550531 Uploaded
bgruening
parents:
diff changeset
57
652f9d550531 Uploaded
bgruening
parents:
diff changeset
58 The above copyright notice and this permission notice shall be included in
652f9d550531 Uploaded
bgruening
parents:
diff changeset
59 all copies or substantial portions of the Software.
652f9d550531 Uploaded
bgruening
parents:
diff changeset
60
652f9d550531 Uploaded
bgruening
parents:
diff changeset
61 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
652f9d550531 Uploaded
bgruening
parents:
diff changeset
62 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
652f9d550531 Uploaded
bgruening
parents:
diff changeset
63 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
652f9d550531 Uploaded
bgruening
parents:
diff changeset
64 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
652f9d550531 Uploaded
bgruening
parents:
diff changeset
65 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
652f9d550531 Uploaded
bgruening
parents:
diff changeset
66 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
652f9d550531 Uploaded
bgruening
parents:
diff changeset
67 THE SOFTWARE.