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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 09:59:46 -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 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
17 Medical Center (Rotterdam, Netherlands) on behalf of the Translational
18 Research IT (TraIT) project:
19
20 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
21
22 More tools by the Translational Research IT (TraIT) project can be found in the following repository:
23
24 http://toolshed.dtls.nl/
25
26 License
27 -------
28
29 **VarScan2**:
30
31 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
32
33 **samtools**:
34
35 MIT/Expat License: https://raw.githubusercontent.com/samtools/samtools/develop/LICENSE
36
37 The MIT/Expat License
38
39 Copyright (C) 2008-2014 Genome Research Ltd.
40
41 Permission is hereby granted, free of charge, to any person obtaining a copy
42 of this software and associated documentation files (the "Software"), to deal
43 in the Software without restriction, including without limitation the rights
44 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
45 copies of the Software, and to permit persons to whom the Software is
46 furnished to do so, subject to the following conditions:
47
48 The above copyright notice and this permission notice shall be included in
49 all copies or substantial portions of the Software.
50
51 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
52 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
53 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
54 THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
55 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
56 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
57 DEALINGS IN THE SOFTWARE.
58
59 [The use of a range of years within a copyright notice in this distribution
60 should be interpreted as being equivalent to a list of years including the
61 first and last year specified and all consecutive years between them.
62
63 For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,
64 2011-2012" should be interpreted as being identical to a notice that reads
65 "Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice
66 that reads "Copyright (C) 2005-2012" should be interpreted as being identical
67 to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,
68 2011, 2012".]
69
70 **samtools-parallel-mpileup**:
71
72 MIT License: https://raw.githubusercontent.com/mydatascience/parallel-mpileup/master/samtools-0.1.19/COPYING
73
74 MIT License:
75
76 Copyright (c) 2008-2009 Genome Research Ltd.
77
78 Permission is hereby granted, free of charge, to any person obtaining a copy
79 of this software and associated documentation files (the "Software"), to deal
80 in the Software without restriction, including without limitation the rights
81 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
82 copies of the Software, and to permit persons to whom the Software is
83 furnished to do so, subject to the following conditions:
84
85 The above copyright notice and this permission notice shall be included in
86 all copies or substantial portions of the Software.
87
88 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
89 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
90 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
91 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
92 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
93 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
94 THE SOFTWARE.
95
96 **This wrapper**:
97
98 Copyright (C) 2013-2014 Youri Hoogstrate
99
100 This program is free software: you can redistribute it and/or modify
101 it under the terms of the GNU General Public License as published by
102 the Free Software Foundation, either version 3 of the License, or
103 (at your option) any later version.
104
105 This program is distributed in the hope that it will be useful,
106 but WITHOUT ANY WARRANTY; without even the implied warranty of
107 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
108 GNU General Public License for more details.
109
110 You should have received a copy of the GNU General Public License
111 along with this program. If not, see <http://www.gnu.org/licenses/>.