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1 Galaxy tool to extract top BLAST hit descriptions from BLAST XML
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2 ================================================================
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3
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4 This tool is copyright 2012-2013 by Peter Cock, The James Hutton Institute
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5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
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6 See the licence text below.
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7
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8 This tool is a short Python script to parse a BLAST XML file, and extract the
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9 identifiers with description for the top matches (by default the top 3), and
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10 output these as a simple tabular file along with the query identifiers.
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11
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12 It is available from the Galaxy Tool Shed at:
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13 http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
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14
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15 This requires the 'blast_datatypes' repository from the Galaxy Tool Shed
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16 to provide the 'blastxml' file format definition.
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17
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18
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19 Automated Installation
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20 ======================
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21
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22 This should be straightforward, Galaxy should automatically install the
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23 'blast_datatypes' dependency.
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24
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25
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26 Manual Installation
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27 ===================
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28
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29 If you haven't done so before, first install the 'blast_datatypes' repository.
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30
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31 There are just two files to install (if doing this manually):
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32
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33 * blastxml_to_top_descr.py (the Python script)
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34 * blastxml_to_top_descr.xml (the Galaxy tool definition)
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35
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36 The suggested location is in the Galaxy folder tools/ncbi_blast_plus next to
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37 the NCBI BLAST+ tool wrappers.
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38
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39 You will also need to modify the tools_conf.xml file to tell Galaxy to offer
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40 the tool. e.g. next to the NCBI BLAST+ tools. Simply add the line::
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41
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42 <tool file="filters/seq_select_by_id.xml" />
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43
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44 To run the tool's tests, also add this line to tools_conf.xml.sample then::
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45
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46 $ sh run_functional_tests.sh -id blastxml_to_top_descr
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47
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48
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49 History
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50 =======
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51
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52 ======= ======================================================================
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53 Version Changes
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54 ------- ----------------------------------------------------------------------
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55 v0.0.1 - Initial version.
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56 v0.0.2 - Since BLAST+ was moved out of the Galaxy core, now have a dependency
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57 on the 'blast_datatypes' repository in the Tool Shed.
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58 v0.0.3 - Include the test files required to run the unit tests
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59 v0.0.4 - Quote filenames in case they contain spaces (internal change)
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60 v0.0.5 - Include number of queries with BLAST matches in stdout (peek text)
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61 v0.0.6 - Check for errors via the script's return code (internal change)
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62 v0.0.7 - Link to Tool Shed added to help text and this documentation.
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63 - Tweak dependency on blast_datatypes to also work on Test Tool Shed
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64 - Adopt standard MIT License.
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65 ======= ======================================================================
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66
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67
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68 Developers
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69 ==========
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70
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71 This script and related tools are being developed on the following hg branch:
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72 http://bitbucket.org/peterjc/galaxy-central/src/tools
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73
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74 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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75 the following command from the Galaxy root folder::
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76
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77 $ tar -czf blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.* tools/ncbi_blast_plus/repository_dependencies.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_top3.tabular
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78
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79 Check this worked::
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80
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81 $ tar -tzf blastxml_to_top_descr.tar.gz
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82 tools/ncbi_blast_plus/blastxml_to_top_descr.py
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83 tools/ncbi_blast_plus/blastxml_to_top_descr.rst
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84 tools/ncbi_blast_plus/blastxml_to_top_descr.xml
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85 tools/ncbi_blast_plus/repository_dependencies.xml
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86 test-data/blastp_four_human_vs_rhodopsin.xml
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87 test-data/blastp_four_human_vs_rhodopsin_top3.tabular
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88
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89
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90 Licence (MIT)
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91 =============
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92
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93 Permission is hereby granted, free of charge, to any person obtaining a copy
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94 of this software and associated documentation files (the "Software"), to deal
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95 in the Software without restriction, including without limitation the rights
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96 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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97 copies of the Software, and to permit persons to whom the Software is
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98 furnished to do so, subject to the following conditions:
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99
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100 The above copyright notice and this permission notice shall be included in
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101 all copies or substantial portions of the Software.
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102
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103 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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104 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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105 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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106 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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107 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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108 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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109 THE SOFTWARE.
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