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comparison tools/effectiveT3/README.rst @ 6:0f6eb4a75000 draft

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v0.0.15 internal changes; v0.0.14 fixed error handling
author peterjc
date Wed, 05 Aug 2015 11:04:42 -0400
parents 1ea715da1879
children 5f85301d50bf
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5:1ea715da1879 6:0f6eb4a75000
1 Galaxy wrapper for EffectiveT3 v1.0.1 1 Galaxy wrapper for EffectiveT3 v1.0.1
2 ===================================== 2 =====================================
3 3
4 This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute 4 This wrapper is copyright 2011-2015 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below. 6 See the licence text below.
7 7
8 This is a wrapper for the command line Java tool EffectiveT3, v1.0.1, 8 This is a wrapper for the command line Java tool EffectiveT3, v1.0.1,
9 9
84 - Use reStructuredText for this README file. 84 - Use reStructuredText for this README file.
85 - Updated citation information (Cock et al. 2013). 85 - Updated citation information (Cock et al. 2013).
86 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy 86 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
87 v0.0.13 - Relax unit test to allow for small floating point score difference. 87 v0.0.13 - Relax unit test to allow for small floating point score difference.
88 - Tool definition now embeds citation information. 88 - Tool definition now embeds citation information.
89 - Fixed error handling in ``effectiveT3.py``. 89 v0.0.14 - Fixed error handling in ``effectiveT3.py``.
90 v0.0.15 - Reorder XML elements (internal change only).
91 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
90 ======= ====================================================================== 92 ======= ======================================================================
91 93
92 94
93 Developers 95 Developers
94 ========== 96 ==========
97 http://bitbucket.org/peterjc/galaxy-central/src/tools 99 http://bitbucket.org/peterjc/galaxy-central/src/tools
98 100
99 Development has now moved to a dedicated GitHub repository: 101 Development has now moved to a dedicated GitHub repository:
100 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 102 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
101 103
102 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use 104 For pushing a release to the test or main "Galaxy Tool Shed", use the following
103 the following command from the Galaxy root folder:: 105 Planemo commands (which requires you have set your Tool Shed access details in
106 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
104 107
105 $ tar -czf effectiveT3.tar.gz tools/effectiveT3/README.rst tools/effectiveT3/effectiveT3.xml tools/effectiveT3/effectiveT3.py tools/effectiveT3/tool_dependencies.xml tool-data/effectiveT3.loc.sample test-data/four_human_proteins.fasta test-data/four_human_proteins.effectiveT3.tabular test-data/empty.fasta test-data/empty_effectiveT3.tabular 108 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/effectiveT3/
109 ...
106 110
111 or::
107 112
108 Check this worked:: 113 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/effectiveT3/
114 ...
109 115
110 $ tar -tzf effectiveT3.tar.gz 116 To just build and check the tar ball, use::
111 tools/effectiveT3/README.rst 117
112 tools/effectiveT3/effectiveT3.xml 118 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/effectiveT3/
113 tools/effectiveT3/effectiveT3.py 119 ...
114 tools/effectiveT3/tool_dependencies.xml 120 $ tar -tzf shed_upload.tar.gz
115 tool-data/effectiveT3.loc.sample 121 tool-data/effectiveT3.loc.sample
122 test-data/empty.fasta
123 test-data/empty_effectiveT3.tabular
116 test-data/four_human_proteins.fasta 124 test-data/four_human_proteins.fasta
117 test-data/four_human_proteins.effectiveT3.tabular 125 test-data/four_human_proteins.effectiveT3.tabular
118 test-data/empty.fasta 126 tool-data/effectiveT3.loc.sample
119 test-data/empty_effectiveT3.tabular 127 tools/effectiveT3/README.rst
128 tools/effectiveT3/effectiveT3.py
129 tools/effectiveT3/effectiveT3.xml
130 tools/effectiveT3/tool_dependencies.xml
120 131
121 132
122 Licence (MIT) 133 Licence (MIT)
123 ============= 134 =============
124 135