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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
author yhoogstrate
date Thu, 05 Nov 2015 10:00:19 -0500
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1 VarScan2 mpileup2snp wrapper for Galaxy
2 =======================================
3
4 http://sourceforge.net/projects/varscan/
5
6 This wrapper is optimized for direct access to BAM files such that the
7 big mpileup files are not saved.
8
9 Development
10 -----------
11
12 Repository-Maintainer: Youri Hoogstrate
13
14 Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
15
16
17 License
18 -------
19
20 **VarScan2**:
21
22 Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0): http://sourceforge.net/directory/os:linux/license:nposl3/freshness:recently-updated/ http://opensource.org/licenses/NPOSL-3.0
23
24 **samtools**:
25
26 MIT/Expat License: https://raw.githubusercontent.com/samtools/samtools/develop/LICENSE
27
28 The MIT/Expat License
29
30 Copyright (C) 2008-2014 Genome Research Ltd.
31
32 Permission is hereby granted, free of charge, to any person obtaining a copy
33 of this software and associated documentation files (the "Software"), to deal
34 in the Software without restriction, including without limitation the rights
35 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
36 copies of the Software, and to permit persons to whom the Software is
37 furnished to do so, subject to the following conditions:
38
39 The above copyright notice and this permission notice shall be included in
40 all copies or substantial portions of the Software.
41
42 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
43 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
44 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
45 THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
46 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
47 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
48 DEALINGS IN THE SOFTWARE.
49
50 [The use of a range of years within a copyright notice in this distribution
51 should be interpreted as being equivalent to a list of years including the
52 first and last year specified and all consecutive years between them.
53
54 For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,
55 2011-2012" should be interpreted as being identical to a notice that reads
56 "Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice
57 that reads "Copyright (C) 2005-2012" should be interpreted as being identical
58 to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,
59 2011, 2012".]
60
61 **samtools-parallel-mpileup**:
62
63 MIT License: https://raw.githubusercontent.com/mydatascience/parallel-mpileup/master/samtools-0.1.19/COPYING
64
65 The MIT License
66
67 Copyright (c) 2008-2009 Genome Research Ltd.
68
69 Permission is hereby granted, free of charge, to any person obtaining a copy
70 of this software and associated documentation files (the "Software"), to deal
71 in the Software without restriction, including without limitation the rights
72 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
73 copies of the Software, and to permit persons to whom the Software is
74 furnished to do so, subject to the following conditions:
75
76 The above copyright notice and this permission notice shall be included in
77 all copies or substantial portions of the Software.
78
79 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
80 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
81 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
82 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
83 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
84 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
85 THE SOFTWARE.
86
87 **This wrapper**:
88
89 Copyright (C) 2013-2014 Youri Hoogstrate
90
91 This program is free software: you can redistribute it and/or modify
92 it under the terms of the GNU General Public License as published by
93 the Free Software Foundation, either version 3 of the License, or
94 (at your option) any later version.
95
96 This program is distributed in the hope that it will be useful,
97 but WITHOUT ANY WARRANTY; without even the implied warranty of
98 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
99 GNU General Public License for more details.
100
101 You should have received a copy of the GNU General Public License
102 along with this program. If not, see <http://www.gnu.org/licenses/>.