Mercurial > repos > peterjc > seq_select_by_id
diff tools/seq_select_by_id/README.rst @ 6:91f55ee8fea5 draft
v0.0.11; more tests and assorting minor changes
| author | peterjc |
|---|---|
| date | Wed, 13 May 2015 10:56:29 -0400 |
| parents | 1a83f5ab9e95 |
| children | a5602454b0ad |
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--- a/tools/seq_select_by_id/README.rst Thu Nov 21 04:54:59 2013 -0500 +++ b/tools/seq_select_by_id/README.rst Wed May 13 10:56:29 2015 -0400 @@ -1,7 +1,7 @@ Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID =============================================================== -This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute +This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. @@ -36,20 +36,20 @@ There are just two files to install to use this tool from within Galaxy: -* seq_select_by_id.py (the Python script) -* seq_select_by_id.xml (the Galaxy tool definition) +* ``seq_select_by_id.py`` (the Python script) +* ``seq_select_by_id.xml`` (the Galaxy tool definition) -The suggested location is a dedicated tools/seq_select_by_id folder. +The suggested location is a dedicated ``tools/seq_select_by_id`` folder. -You will also need to modify the tools_conf.xml file to tell Galaxy to offer the +You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool. One suggested location is in the filters section. Simply add the line:: <tool file="seq_select_by_id/seq_select_by_id.xml" /> -If you wish to run the unit tests, also add this to tools_conf.xml.sample -and move/copy the test-data files under Galaxy's test-data folder. Then:: +If you wish to run the unit tests, also move/copy the ``test-data/`` files +under Galaxy's ``test-data/`` folder. Then:: - $ ./run_functional_tests.sh -id seq_select_by_id + $ ./run_tests.sh -id seq_select_by_id You will also need to install Biopython 1.54 or later. That's it. @@ -73,7 +73,18 @@ - Fixed Biopython dependency setup. - Development moved to GitHub, https://github.com/peterjc/pico_galaxy - Renamed folder and adopted README.rst naming. -v0.0.8 - Corrected automated dependency definition +v0.0.8 - Corrected automated dependency definition. +v0.0.9 - Simplified XML to apply input format to output data. + - Tool definition now embeds citation information. + - Include input dataset name in output dataset names. + - If white space is found in the requested tabular field then only + the first word is used as the identifier (with a warning to stderr). +v0.0.10 - Includes testing of stdout messages. + - Includes testing of failure modes. +v0.0.11 - Use the ``format_source=...`` tag. + - Reorder XML elements (internal change only). + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). + - Quote filenames in case of spaces (internal change only). ======= ====================================================================== @@ -86,21 +97,31 @@ Development has now moved to a dedicated GitHub repository: https://github.com/peterjc/pico_galaxy/tree/master/tools -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy 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/pico_galaxy/tools/seq_select_by_id/ + ... + +or:: - $ tar -czf seq_select_by_id.tar.gz tools/seq_select_by_id/README.rst tools/seq_select_by_id/seq_select_by_id.* tools/seq_select_by_id/tool_dependencies.xml test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular + $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_select_by_id/ + ... + +To just build and check the tar ball, use:: -Check this worked:: - - $ tar -tzf seq_select_by_id.tar.gz + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/seq_select_by_id/ + ... + $ tar -tzf shed_upload.tar.gz + test-data/k12_hypothetical.fasta + test-data/k12_hypothetical.tabular + test-data/k12_hypothetical_alt.tabular + test-data/k12_ten_proteins.fasta tools/seq_select_by_id/README.rst tools/seq_select_by_id/seq_select_by_id.py tools/seq_select_by_id/seq_select_by_id.xml tools/seq_select_by_id/tool_dependencies.xml - test-data/k12_ten_proteins.fasta - test-data/k12_hypothetical.fasta - test-data/k12_hypothetical.tabular Licence (MIT)