Mercurial > repos > peterjc > blastxml_to_top_descr

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.

It is available from the Galaxy Tool Shed at:
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr

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)
v0.0.5 - Include number of queries with BLAST matches in stdout (peek text)
v0.0.6 - Check for errors via the script's return code (internal change)
v0.0.7 - Link to Tool Shed added to help text and this documentation.
       - Tweak dependency on blast_datatypes too also work on Test Tool Shed


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://toolshed.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.
author	peterjc
date	Mon, 20 May 2013 10:00:09 -0400
parents	58359ce5bde9
children	482b7f4d3587