blastxml_to_top_descr: tools/blastxml_to_top

comparison 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

comparison

equal deleted inserted replaced

-:fe1ed74793c9
+:8dc4ba7eba5d
 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.
 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
+This requires the ``blast_datatypes`` repository from the Galaxy Tool Shed
-to provide the 'blastxml' file format definition.
+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.py`` (the Python script)
-* blastxml_to_top_descr.xml (the Galaxy tool definition)
+- ``blastxml_to_top_descr.xml`` (the Galaxy tool definition)
-The suggested location is in the Galaxy folder tools/ncbi_blast_plus next to
+The suggested location is in the Galaxy folder ``tools/ncbi_blast_plus/``
-the NCBI BLAST+ tool wrappers.
+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
 =======
 ======= ======================================================================
 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.
+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).
 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
 ===========
 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 making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
-the following command from the GitHub repository root folder::
+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)::
-$ 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 testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blastxml_to_top_descr/
+...
-Check this worked::
+or::
-$ tar -tzf blastxml_to_top_descr.tar.gz
+$ 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
-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)
 =============

Mercurial > repos > peterjc > blastxml_to_top_descr

comparison tools/blastxml_to_top_descr/README.rst @ 13:8dc4ba7eba5d draft default tip