Mercurial > repos > peterjc > align_back_trans

comparison tools/align_back_trans/README.rst @ 2:9fbf29a8c12b draft

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v0.0.6 use format_source; v0.0.5 more explicit error msg, citation info
author peterjc
date Wed, 05 Aug 2015 10:52:56 -0400
parents ec202446408a
children de803005027f
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1:ec202446408a 2:9fbf29a8c12b
1 Galaxy tool to back-translate a protein alignment to nucleotides 1 Galaxy tool to back-translate a protein alignment to nucleotides
2 ================================================================ 2 ================================================================
3 3
4 This tool is copyright 2012-2014 by Peter Cock, The James Hutton Institute 4 This tool is copyright 2012-2015 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 (MIT licence). 6 See the licence text below (MIT licence).
7 7
8 This tool is a short Python script (using Biopython library functions) to 8 This tool is a short Python script (using Biopython library functions) to
9 load a protein alignment, and matching nucleotide FASTA file of unaligned 9 load a protein alignment, and matching nucleotide FASTA file of unaligned
41 the tool. One suggested location is in the multiple alignments section. Simply 41 the tool. One suggested location is in the multiple alignments section. Simply
42 add the line:: 42 add the line::
43 43
44 <tool file="align_back_trans/align_back_trans.xml" /> 44 <tool file="align_back_trans/align_back_trans.xml" />
45 45
46 You will also need to install Biopython 1.62 or later. If you want to run 46 You will also need to install Biopython 1.62 or later.
47 the unit tests, include this line in ``tools_conf.xml.sample`` and the sample
48 FASTA files under the ``test-data`` directory. Then::
49 47
50 ./run_functional_tests.sh -id align_back_trans 48 If you wish to run the unit tests, also move/copy the ``test-data/`` files
49 under Galaxy's ``test-data/`` folder. Then::
50
51 ./run_tests.sh -id align_back_trans
51 52
52 That's it. 53 That's it.
53 54
54 55
55 History 56 History
61 v0.0.1 - Initial version, based on a previously written Python script 62 v0.0.1 - Initial version, based on a previously written Python script
62 v0.0.2 - Optionally check the translation is consistent 63 v0.0.2 - Optionally check the translation is consistent
63 v0.0.3 - First official release 64 v0.0.3 - First official release
64 v0.0.4 - Simplified XML to apply input format to output data. 65 v0.0.4 - Simplified XML to apply input format to output data.
65 - Fixed error message when sequence length not a multiple of three. 66 - Fixed error message when sequence length not a multiple of three.
67 v0.0.5 - More explicit error messages when seqences lengths do not match.
68 - Tool definition now embeds citation information.
69 v0.0.6 - Reorder XML elements (internal change only).
70 - Use ``format_source=...`` tag.
71 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
66 ======= ====================================================================== 72 ======= ======================================================================
67 73
68 74
69 Developers 75 Developers
70 ========== 76 ==========
73 https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py 79 https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py
74 80
75 With the addition of a Galaxy wrapper, developement moved here: 81 With the addition of a Galaxy wrapper, developement moved here:
76 https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans 82 https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
77 83
78 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use 84 For pushing a release to the test or main "Galaxy Tool Shed", use the following
79 the following command from the Galaxy root folder:: 85 Planemo commands (which requires you have set your Tool Shed access details in
86 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
80 87
81 $ tar -czf align_back_trans.tar.gz tools/align_back_trans/README.rst tools/align_back_trans/align_back_trans.py tools/align_back_trans/align_back_trans.xml tools/align_back_trans/tool_dependencies.xml test-data/demo_nucs.fasta test-data/demo_nucs_trailing_stop.fasta test-data/demo_prot_align.fasta test-data/demo_nuc_align.fasta 88 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
89 ...
82 90
83 Check this worked:: 91 or::
84 92
85 $ tar -tzf align_back_trans.tar.gz 93 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
94 ...
95
96 To just build and check the tar ball, use::
97
98 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/align_back_trans/
99 ...
100 $ tar -tzf shed_upload.tar.gz
101 test-data/demo_nucs.fasta
102 test-data/demo_nucs_trailing_stop.fasta
103 test-data/demo_prot_align.fasta
104 test-data/demo_nuc_align.fasta
86 tools/align_back_trans/README.rst 105 tools/align_back_trans/README.rst
87 tools/align_back_trans/align_back_trans.py 106 tools/align_back_trans/align_back_trans.py
88 tools/align_back_trans/align_back_trans.xml 107 tools/align_back_trans/align_back_trans.xml
89 tools/align_back_trans/tool_dependencies.xml 108 tools/align_back_trans/tool_dependencies.xml
90 test-data/demo_nucs.fasta
91 test-data/demo_nucs_trailing_stop.fasta
92 test-data/demo_prot_align.fasta
93 test-data/demo_nuc_align.fasta
94 109
95 110
96 Licence (MIT) 111 Licence (MIT)
97 ============= 112 =============
98 113