Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
annotate README.rst @ 1:9a39c4105901 draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
author | erasmus-medical-center |
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date | Wed, 15 Feb 2017 16:16:01 -0500 |
parents | 0c5cc5763091 |
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0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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1 VarScan2 mpileup2snp wrapper for Galaxy |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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2 ======================================= |
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3 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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4 http://sourceforge.net/projects/varscan/ |
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5 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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6 This wrapper is optimized for direct access to BAM files such that the |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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7 big mpileup files are not saved. |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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8 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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9 Development |
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10 ----------- |
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11 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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12 * Repository-Maintainer: Youri Hoogstrate |
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13 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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14 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools |
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15 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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16 The tool wrapper has been written by Youri Hoogstrate from the Erasmus |
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17 Medical Center (Rotterdam, Netherlands) on behalf of the Translational |
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18 Research IT (TraIT) project: |
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19 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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20 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch |
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21 |
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22 More tools by the Translational Research IT (TraIT) project can be found in the following repository: |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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23 |
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24 http://toolshed.dtls.nl/ |
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25 |
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26 License |
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27 ------- |
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28 |
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29 **VarScan2**: |
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30 |
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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 |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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32 |
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33 **samtools**: |
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34 |
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35 MIT/Expat License: https://raw.githubusercontent.com/samtools/samtools/develop/LICENSE |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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36 |
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37 The MIT/Expat License |
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38 |
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39 Copyright (C) 2008-2014 Genome Research Ltd. |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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40 |
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41 Permission is hereby granted, free of charge, to any person obtaining a copy |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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42 of this software and associated documentation files (the "Software"), to deal |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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43 in the Software without restriction, including without limitation the rights |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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44 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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45 copies of the Software, and to permit persons to whom the Software is |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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46 furnished to do so, subject to the following conditions: |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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47 |
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48 The above copyright notice and this permission notice shall be included in |
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49 all copies or substantial portions of the Software. |
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50 |
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51 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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52 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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53 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL |
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54 THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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55 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING |
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56 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER |
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57 DEALINGS IN THE SOFTWARE. |
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58 |
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59 [The use of a range of years within a copyright notice in this distribution |
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60 should be interpreted as being equivalent to a list of years including the |
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61 first and last year specified and all consecutive years between them. |
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62 |
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63 For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009, |
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64 2011-2012" should be interpreted as being identical to a notice that reads |
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65 "Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice |
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66 that reads "Copyright (C) 2005-2012" should be interpreted as being identical |
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67 to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010, |
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68 2011, 2012".] |
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69 |
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70 **samtools-parallel-mpileup**: |
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71 |
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72 MIT License: https://raw.githubusercontent.com/mydatascience/parallel-mpileup/master/samtools-0.1.19/COPYING |
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73 |
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74 MIT License: |
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75 |
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76 Copyright (c) 2008-2009 Genome Research Ltd. |
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77 |
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78 Permission is hereby granted, free of charge, to any person obtaining a copy |
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79 of this software and associated documentation files (the "Software"), to deal |
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80 in the Software without restriction, including without limitation the rights |
0c5cc5763091
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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81 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
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82 copies of the Software, and to permit persons to whom the Software is |
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83 furnished to do so, subject to the following conditions: |
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84 |
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85 The above copyright notice and this permission notice shall be included in |
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86 all copies or substantial portions of the Software. |
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87 |
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88 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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89 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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90 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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91 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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92 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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93 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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94 THE SOFTWARE. |
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95 |
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96 **This wrapper**: |
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97 |
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98 Copyright (C) 2013-2014 Youri Hoogstrate |
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99 |
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100 This program is free software: you can redistribute it and/or modify |
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101 it under the terms of the GNU General Public License as published by |
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102 the Free Software Foundation, either version 3 of the License, or |
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103 (at your option) any later version. |
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104 |
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105 This program is distributed in the hope that it will be useful, |
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106 but WITHOUT ANY WARRANTY; without even the implied warranty of |
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107 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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108 GNU General Public License for more details. |
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109 |
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110 You should have received a copy of the GNU General Public License |
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111 along with this program. If not, see <http://www.gnu.org/licenses/>. |