Mercurial > repos > peterjc > blastxml_to_top_descr
view tools/ncbi_blast_plus/blastxml_to_top_descr.txt @ 5:662fea0fe6b2 draft
Uploaded v0.0.4, quotes filenames in case the contain spaces
author | peterjc |
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date | Wed, 20 Feb 2013 13:36:37 -0500 |
parents | 34a0adda2770 |
children | 8a0771c5e236 |
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Galaxy tool to extract top BLAST hit descriptions from BLAST XML ================================================================ This tool is copyright 2012-2013 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. This tool is a short Python script to parse a BLAST XML file, and extract the identifiers with description for the top matches (by default the top 3), and output these as a simple tabular file along with the query identifiers. This requires the 'blast_datatypes' repository from the Galaxy Tool Shed to provide the 'blastxml' file format definition. Automated Installation ====================== This should be straightforward, Galaxy should automatically install the 'blast_datatypes' dependency. Manual Installation =================== If you haven't done so before, first install the 'blast_datatypes' repository. There are just two files to install (if doing this manually): * blastxml_to_top_descr.py (the Python script) * blastxml_to_top_descr.xml (the Galaxy tool definition) The suggested location is in the Galaxy folder tools/ncbi_blast_plus next to the NCBI BLAST+ tool wrappers. You will also need to modify the tools_conf.xml file to tell Galaxy to offer the tool. e.g. next to the NCBI BLAST+ tools. Simply add the line: <tool file="filters/seq_select_by_id.xml" /> To run the tool's tests, also add this line to tools_conf.xml.sample then: $ sh run_functional_tests.sh -id blastxml_to_top_descr History ======= v0.0.1 - Initial version. v0.0.2 - Since BLAST+ was moved out of the Galaxy core, now have a dependency on the 'blast_datatypes' repository in the Tool Shed. v0.0.3 - Include the test files required to run the unit tests v0.0.4 - Quote filenames in case they contain spaces (internal change) Developers ========== This script and related tools are being developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: $ 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 Check this worked: $ tar -tzf blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.py tools/ncbi_blast_plus/blastxml_to_top_descr.txt tools/ncbi_blast_plus/blastxml_to_top_descr.xml tools/ncbi_blast_plus/repository_dependencies.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_top3.tabular Licence (MIT/BSD style) ======================= Permission to use, copy, modify, and distribute this software and its documentation with or without modifications and for any purpose and without fee is hereby granted, provided that any copyright notices appear in all copies and that both those copyright notices and this permission notice appear in supporting documentation, and that the names of the contributors or copyright holders not be used in advertising or publicity pertaining to distribution of the software without specific prior permission. THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.