Mercurial > repos > peterjc > blastxml_to_top_descr
diff 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 |
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children | dff89c7e4308 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/blastxml_to_top_descr.txt Thu Feb 07 14:56:18 2013 -0500 @@ -0,0 +1,79 @@ +Galaxy tool to extract top BLAST hit descriptions from BLAST XML +================================================================ + +This tool is copyright 2012 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. + +There are no additional dependancies. + + +Manual Installation +=================== + +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. + + +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.* + +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 + +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.