Mercurial > repos > peterjc > blastxml_to_top_descr
changeset 14:b46c041afbe4 draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/blastxml_to_top_descr commit 87df4063e559fe6a4db806a52d657404c2ad766c
| author | peterjc |
|---|---|
| date | Fri, 15 May 2015 05:56:41 -0400 |
| parents | 796dc2ff8e8e |
| children | 60d0c6c1a71f |
| files | test-data/blastp_four_human_vs_rhodopsin.xml 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 |
| diffstat | 5 files changed, 48 insertions(+), 40 deletions(-) [+] |
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--- a/test-data/blastp_four_human_vs_rhodopsin.xml Wed Jul 30 05:38:46 2014 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Fri May 15 05:56:41 2015 -0400 @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastp</BlastOutput_program> - <BlastOutput_version>BLASTP 2.2.29+</BlastOutput_version> + <BlastOutput_version>BLASTP 2.2.30+</BlastOutput_version> <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>sp|Q9BS26|ERP44_HUMAN</BlastOutput_query-ID>
--- a/tools/blastxml_to_top_descr/README.rst Wed Jul 30 05:38:46 2014 -0400 +++ b/tools/blastxml_to_top_descr/README.rst Fri May 15 05:56:41 2015 -0400 @@ -1,7 +1,7 @@ -Galaxy tool to extract top BLAST hit descriptions from BLAST XML +OBGalaxy 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 +71,8 @@ - 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). ======= ====================================================================== @@ -89,22 +92,31 @@ 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_upload --shed_target 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_upload --shed_target 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)
--- a/tools/blastxml_to_top_descr/blastxml_to_top_descr.py Wed Jul 30 05:38:46 2014 -0400 +++ b/tools/blastxml_to_top_descr/blastxml_to_top_descr.py Fri May 15 05:56:41 2015 -0400 @@ -12,7 +12,7 @@ from optparse import OptionParser if "-v" in sys.argv or "--version" in sys.argv: - print "v0.1.0" + print "v0.1.1" sys.exit(0) if sys.version_info[:2] >= ( 2, 5 ): @@ -105,8 +105,8 @@ """ current_query = None current_hits = [] - with open(in_file) as input: - for line in input: + with open(in_file) as input_handle: + for line in input_handle: parts = line.rstrip("\n").split("\t") query = parts[qseqid] descr = "%s %s" % (parts[sseqid], parts[salltitles]) @@ -157,8 +157,6 @@ assert not re_default_subject_id.match("Subject_12a") assert not re_default_subject_id.match("TheSubject_1") - count = 0 - pos_count = 0 current_query = None hit_descrs = [] for event, elem in context:
--- a/tools/blastxml_to_top_descr/blastxml_to_top_descr.xml Wed Jul 30 05:38:46 2014 -0400 +++ b/tools/blastxml_to_top_descr/blastxml_to_top_descr.xml Fri May 15 05:56:41 2015 -0400 @@ -1,5 +1,10 @@ -<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.1.1"> +<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.1.2"> <description>Make a table from BLAST output</description> + <stdio> + <!-- Assume anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command> <command interpreter="python"> blastxml_to_top_descr.py @@ -13,11 +18,6 @@ -t ${topN} "${in_file}" </command> - <stdio> - <!-- Assume anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> <inputs> <conditional name="input"> <param name="in_format" type="select" label="Input format"> @@ -48,8 +48,6 @@ <outputs> <data name="tabular_file" format="tabular" label="Top $topN descriptions from $input.in_file.name" /> </outputs> - <requirements> - </requirements> <tests> <test> <param name="in_format" value="blastxml" />
--- a/tools/blastxml_to_top_descr/repository_dependencies.xml Wed Jul 30 05:38:46 2014 -0400 +++ b/tools/blastxml_to_top_descr/repository_dependencies.xml Fri May 15 05:56:41 2015 -0400 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="Requires BLAST XML and database datatype definitions."> -<repository changeset_revision="939a600f45e9" name="blast_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> +<repository changeset_revision="da92fef90117" name="blast_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>