Mercurial > repos > peterjc > blastxml_to_top_descr
diff tools/blastxml_to_top_descr/README.rst @ 13:8dc4ba7eba5d draft default tip
v0.1.2 with Python 3.9 declaration
| author | peterjc |
|---|---|
| date | Sun, 17 Sep 2023 13:01:56 +0000 |
| parents | fe1ed74793c9 |
| children |
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--- a/tools/blastxml_to_top_descr/README.rst Wed Jul 30 05:36:52 2014 -0400 +++ b/tools/blastxml_to_top_descr/README.rst Sun Sep 17 13:01:56 2023 +0000 @@ -1,7 +1,7 @@ Galaxy tool to extract top BLAST hit descriptions from BLAST XML ================================================================ -This tool is copyright 2012-2013 by Peter Cock, The James Hutton Institute +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. @@ -12,38 +12,39 @@ 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. +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. +``blast_datatypes`` dependency. Manual Installation =================== -If you haven't done so before, first install the 'blast_datatypes' repository. +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) +- ``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. +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 +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" /> -To run the tool's tests, also add this line to tools_conf.xml.sample then:: +If you wish to run the unit tests, alsomove/copy the ``test-data/`` files +under Galaxy's ``test-data/`` folder. Then:: - $ sh run_functional_tests.sh -id blastxml_to_top_descr + $ sh run_tests.sh -id blastxml_to_top_descr History @@ -54,13 +55,13 @@ ------- ---------------------------------------------------------------------- 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. + 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 + - 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). @@ -70,6 +71,11 @@ - 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. ======= ====================================================================== @@ -89,22 +95,31 @@ As of July 2013, development is continuing on a dedicated GitHub repository: https://github.com/peterjc/galaxy_blast -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the GitHub repository root folder:: +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:: - $ tar -czf blastxml_to_top_descr.tar.gz tools/blastxml_to_top_descr/README.rst tools/blastxml_to_top_descr/blastxml_to_top_descr.* tools/blastxml_to_top_descr/repository_dependencies.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_top3.tabular test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular + $ planemo shed_update -t toolshed --check_diff ~/repositories/galaxy_blast/tools/blastxml_to_top_descr/ + ... + +To just build and check the tar ball, use:: -Check this worked:: - - $ tar -tzf blastxml_to_top_descr.tar.gz + $ 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 - test-data/blastp_four_human_vs_rhodopsin.xml - test-data/blastp_four_human_vs_rhodopsin_top3.tabular - test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular - test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular Licence (MIT)