Mercurial > repos > peterjc > blastxml_to_top_descr
changeset 8:a8ef75aab1f9 draft
Uploaded v0.0.7, README style updated, MIT license
| author | peterjc |
|---|---|
| date | Wed, 24 Jul 2013 11:56:22 -0400 |
| parents | a7add03a44fd |
| children | 6aafa0ced802 |
| files | tools/ncbi_blast_plus/blastxml_to_top_descr.rst 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 |
| diffstat | 4 files changed, 117 insertions(+), 102 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/blastxml_to_top_descr.rst Wed Jul 24 11:56:22 2013 -0400 @@ -0,0 +1,109 @@ +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 +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +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 to also work on Test Tool Shed + - Adopt standard MIT License. +======= ====================================================================== + + +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.rst + 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) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE.
--- a/tools/ncbi_blast_plus/blastxml_to_top_descr.txt Wed Apr 17 11:46:03 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,99 +0,0 @@ -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) -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) - - -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.
--- a/tools/ncbi_blast_plus/blastxml_to_top_descr.xml Wed Apr 17 11:46:03 2013 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_top_descr.xml Wed Jul 24 11:56:22 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.6"> +<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.7"> <description>Make a table from BLAST XML</description> <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command> <command interpreter="python"> @@ -49,5 +49,10 @@ to spot some problems (e.g. bacterial contaimination could be very obvious). +**Citation** + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr + </help> </tool>
--- a/tools/ncbi_blast_plus/repository_dependencies.xml Wed Apr 17 11:46:03 2013 -0400 +++ b/tools/ncbi_blast_plus/repository_dependencies.xml Wed Jul 24 11:56:22 2013 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> <repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format)."> -<!-- Revision 4:f9a7783ed7b6 on the main tool shed is v0.0.14 which added BLAST databases --> -<repository toolshed="http://toolshed.g2.bx.psu.edu" name="blast_datatypes" owner="devteam" changeset_revision="f9a7783ed7b6" /> +<!-- Revision 4:f9a7783ed7b6 on the main (and test) tool shed is v0.0.14 which added BLAST databases --> +<repository changeset_revision="f9a7783ed7b6" name="blast_datatypes" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> </repositories>