Mercurial > repos > peterjc > blastxml_to_top_descr
comparison tools/ncbi_blast_plus/blastxml_to_top_descr.txt @ 0:075fe5424c32 draft
Uploaded v0.0.1
| author | peterjc |
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| date | Thu, 07 Feb 2013 14:56:18 -0500 |
| parents | |
| children | dff89c7e4308 |
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| -1:000000000000 | 0:075fe5424c32 |
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| 1 Galaxy tool to extract top BLAST hit descriptions from BLAST XML | |
| 2 ================================================================ | |
| 3 | |
| 4 This tool is copyright 2012 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 There are no additional dependancies. | |
| 13 | |
| 14 | |
| 15 Manual Installation | |
| 16 =================== | |
| 17 | |
| 18 There are just two files to install (if doing this manually): | |
| 19 | |
| 20 * blastxml_to_top_descr.py (the Python script) | |
| 21 * blastxml_to_top_descr.xml (the Galaxy tool definition) | |
| 22 | |
| 23 The suggested location is in the Galaxy folder tools/ncbi_blast_plus next to | |
| 24 the NCBI BLAST+ tool wrappers. | |
| 25 | |
| 26 You will also need to modify the tools_conf.xml file to tell Galaxy to offer | |
| 27 the tool. e.g. next to the NCBI BLAST+ tools. Simply add the line: | |
| 28 | |
| 29 <tool file="filters/seq_select_by_id.xml" /> | |
| 30 | |
| 31 To run the tool's tests, also add this line to tools_conf.xml.sample then: | |
| 32 | |
| 33 $ sh run_functional_tests.sh -id blastxml_to_top_descr | |
| 34 | |
| 35 | |
| 36 History | |
| 37 ======= | |
| 38 | |
| 39 v0.0.1 - Initial version. | |
| 40 | |
| 41 | |
| 42 Developers | |
| 43 ========== | |
| 44 | |
| 45 This script and related tools are being developed on the following hg branch: | |
| 46 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
| 47 | |
| 48 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use | |
| 49 the following command from the Galaxy root folder: | |
| 50 | |
| 51 $ tar -czf blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.* | |
| 52 | |
| 53 Check this worked: | |
| 54 | |
| 55 $ tar -tzf blastxml_to_top_descr.tar.gz | |
| 56 tools/ncbi_blast_plus/blastxml_to_top_descr.py | |
| 57 tools/ncbi_blast_plus/blastxml_to_top_descr.txt | |
| 58 tools/ncbi_blast_plus/blastxml_to_top_descr.xml | |
| 59 | |
| 60 Licence (MIT/BSD style) | |
| 61 ======================= | |
| 62 | |
| 63 Permission to use, copy, modify, and distribute this software and its | |
| 64 documentation with or without modifications and for any purpose and | |
| 65 without fee is hereby granted, provided that any copyright notices | |
| 66 appear in all copies and that both those copyright notices and this | |
| 67 permission notice appear in supporting documentation, and that the | |
| 68 names of the contributors or copyright holders not be used in | |
| 69 advertising or publicity pertaining to distribution of the software | |
| 70 without specific prior permission. | |
| 71 | |
| 72 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
| 73 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
| 74 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
| 75 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
| 76 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
| 77 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
| 78 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
| 79 OR PERFORMANCE OF THIS SOFTWARE. |