Mercurial > repos > peterjc > blastxml_to_top_descr
comparison tools/ncbi_blast_plus/blastxml_to_top_descr.rst @ 8:a8ef75aab1f9 draft
Uploaded v0.0.7, README style updated, MIT license
author | peterjc |
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date | Wed, 24 Jul 2013 11:56:22 -0400 |
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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="filters/seq_select_by_id.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 ======= ====================================================================== | |
66 | |
67 | |
68 Developers | |
69 ========== | |
70 | |
71 This script and related tools are being developed on the following hg branch: | |
72 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
73 | |
74 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | |
75 the following command from the Galaxy root folder:: | |
76 | |
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 | |
78 | |
79 Check this worked:: | |
80 | |
81 $ tar -tzf blastxml_to_top_descr.tar.gz | |
82 tools/ncbi_blast_plus/blastxml_to_top_descr.py | |
83 tools/ncbi_blast_plus/blastxml_to_top_descr.rst | |
84 tools/ncbi_blast_plus/blastxml_to_top_descr.xml | |
85 tools/ncbi_blast_plus/repository_dependencies.xml | |
86 test-data/blastp_four_human_vs_rhodopsin.xml | |
87 test-data/blastp_four_human_vs_rhodopsin_top3.tabular | |
88 | |
89 | |
90 Licence (MIT) | |
91 ============= | |
92 | |
93 Permission is hereby granted, free of charge, to any person obtaining a copy | |
94 of this software and associated documentation files (the "Software"), to deal | |
95 in the Software without restriction, including without limitation the rights | |
96 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
97 copies of the Software, and to permit persons to whom the Software is | |
98 furnished to do so, subject to the following conditions: | |
99 | |
100 The above copyright notice and this permission notice shall be included in | |
101 all copies or substantial portions of the Software. | |
102 | |
103 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
104 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
105 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
106 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
107 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
108 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
109 THE SOFTWARE. |