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Uploaded v0.1.0, now also handles extended tabular BLAST output.
author peterjc
date Fri, 13 Jun 2014 07:07:35 -0400
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10:09a68a90d552 11:98f8431dab44
1 Galaxy tool to extract top BLAST hit descriptions from BLAST XML
2 ================================================================
3
4 This tool is copyright 2012-2013 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below.
7
8 This tool is a short Python script to parse a BLAST XML file, and extract the
9 identifiers with description for the top matches (by default the top 3), and
10 output these as a simple tabular file along with the query identifiers.
11
12 It is available from the Galaxy Tool Shed at:
13 http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
14
15 This requires the 'blast_datatypes' repository from the Galaxy Tool Shed
16 to provide the 'blastxml' file format definition.
17
18
19 Automated Installation
20 ======================
21
22 This should be straightforward, Galaxy should automatically install the
23 'blast_datatypes' dependency.
24
25
26 Manual Installation
27 ===================
28
29 If you haven't done so before, first install the 'blast_datatypes' repository.
30
31 There are just two files to install (if doing this manually):
32
33 * blastxml_to_top_descr.py (the Python script)
34 * blastxml_to_top_descr.xml (the Galaxy tool definition)
35
36 The suggested location is in the Galaxy folder tools/ncbi_blast_plus next to
37 the NCBI BLAST+ tool wrappers.
38
39 You will also need to modify the tools_conf.xml file to tell Galaxy to offer
40 the tool. e.g. next to the NCBI BLAST+ tools. Simply add the line::
41
42 <tool file="ncbi_blast_plus/blastxml_to_top_descr.xml" />
43
44 To run the tool's tests, also add this line to tools_conf.xml.sample then::
45
46 $ sh run_functional_tests.sh -id blastxml_to_top_descr
47
48
49 History
50 =======
51
52 ======= ======================================================================
53 Version Changes
54 ------- ----------------------------------------------------------------------
55 v0.0.1 - Initial version.
56 v0.0.2 - Since BLAST+ was moved out of the Galaxy core, now have a dependency
57 on the 'blast_datatypes' repository in the Tool Shed.
58 v0.0.3 - Include the test files required to run the unit tests
59 v0.0.4 - Quote filenames in case they contain spaces (internal change)
60 v0.0.5 - Include number of queries with BLAST matches in stdout (peek text)
61 v0.0.6 - Check for errors via the script's return code (internal change)
62 v0.0.7 - Link to Tool Shed added to help text and this documentation.
63 - Tweak dependency on blast_datatypes to also work on Test Tool Shed
64 - Adopt standard MIT License.
65 v0.0.8 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
66 v0.0.9 - Updated citation information (Cock et al. 2013).
67 v0.0.10 - Update help text to mention BLAST+ 2.2.28 can produce tabular files
68 including the description/title (via the salltitles field).
69 v0.1.0 - Switch to using an optparse based API for Python script internally.
70 - Support BLAST XML with multiple ``<Iteration>`` blocks per query.
71 - Support the default 25 column extended tabular BLAST output.
72 ======= ======================================================================
73
74
75 Bug Reports
76 ===========
77
78 You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask
79 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
80
81
82 Developers
83 ==========
84
85 This script and related tools were originally developed on the 'tools' branch of
86 the following Mercurial repository: https://bitbucket.org/peterjc/galaxy-central/
87
88 As of July 2013, development is continuing on a dedicated GitHub repository:
89 https://github.com/peterjc/galaxy_blast
90
91 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
92 the following command from the GitHub repository root folder::
93
94 $ tar -czf blastxml_to_top_descr.tar.gz tools/blastxml_to_top_descr/README.rst tools/blastxml_to_top_descr/blastxml_to_top_descr.* tools/blastxml_to_top_descr/repository_dependencies.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_top3.tabular test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular
95
96 Check this worked::
97
98 $ tar -tzf blastxml_to_top_descr.tar.gz
99 tools/blastxml_to_top_descr/README.rst
100 tools/blastxml_to_top_descr/blastxml_to_top_descr.py
101 tools/blastxml_to_top_descr/blastxml_to_top_descr.xml
102 tools/blastxml_to_top_descr/repository_dependencies.xml
103 test-data/blastp_four_human_vs_rhodopsin.xml
104 test-data/blastp_four_human_vs_rhodopsin_top3.tabular
105 test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular
106 test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular
107
108
109 Licence (MIT)
110 =============
111
112 Permission is hereby granted, free of charge, to any person obtaining a copy
113 of this software and associated documentation files (the "Software"), to deal
114 in the Software without restriction, including without limitation the rights
115 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
116 copies of the Software, and to permit persons to whom the Software is
117 furnished to do so, subject to the following conditions:
118
119 The above copyright notice and this permission notice shall be included in
120 all copies or substantial portions of the Software.
121
122 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
123 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
124 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
125 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
126 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
127 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
128 THE SOFTWARE.