Mercurial > repos > peterjc > blastxml_to_top_descr
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v0.1.2 with Python 3.9 declaration
author | peterjc |
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date | Sun, 17 Sep 2023 13:01:56 +0000 |
parents | fe1ed74793c9 |
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Galaxy tool to extract top BLAST hit descriptions from BLAST XML ================================================================ This tool is copyright 2012-2015 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="ncbi_blast_plus/blastxml_to_top_descr.xml" /> If you wish to run the unit tests, alsomove/copy the ``test-data/`` files under Galaxy's ``test-data/`` folder. Then:: $ sh run_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. v0.0.8 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast v0.0.9 - Updated citation information (Cock et al. 2013). v0.0.10 - Update help text to mention BLAST+ 2.2.28 can produce tabular files including the description/title (via the salltitles field). v0.1.0 - Switch to using an optparse based API for Python script internally. - Support BLAST XML with multiple ``<Iteration>`` blocks per query. - Support the default 25 column extended tabular BLAST output. v0.1.1 - Embed citation information in the tool XML (new Galaxy feature). v0.1.2 - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). - Use ``<command detect_errors="aggressive">`` (internal change only). - Single quote command line arguments (internal change only). - Python 3 compatible syntax. ======= ====================================================================== Bug Reports =========== You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev Developers ========== This script and related tools were originally developed on the 'tools' branch of the following Mercurial repository: https://bitbucket.org/peterjc/galaxy-central/ As of July 2013, development is continuing on a dedicated GitHub repository: https://github.com/peterjc/galaxy_blast For pushing a release to the test or main "Galaxy Tool Shed", use the following Planemo commands (which requires you have set your Tool Shed access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: $ planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blastxml_to_top_descr/ ... or:: $ planemo shed_update -t toolshed --check_diff ~/repositories/galaxy_blast/tools/blastxml_to_top_descr/ ... To just build and check the tar ball, use:: $ planemo shed_upload --tar_only ~/repositories/galaxy_blast/tools/blastxml_to_top_descr/ ... $ tar -tzf shed_upload.tar.gz test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular test-data/blastp_four_human_vs_rhodopsin_top3.tabular test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular tools/blastxml_to_top_descr/README.rst tools/blastxml_to_top_descr/blastxml_to_top_descr.py tools/blastxml_to_top_descr/blastxml_to_top_descr.xml tools/blastxml_to_top_descr/repository_dependencies.xml 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.