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comparison tools/align_back_trans/README.rst @ 0:6c6b16cab42a draft

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author jasper
date Tue, 09 May 2017 13:22:02 -0400
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1 Galaxy tool to back-translate a protein alignment to nucleotides
2 ================================================================
3
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.
6 See the licence text below (MIT licence).
7
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
10 sequences, which are threaded onto the protein alignment in order to produce
11 a codon aware nucleotide alignment - which can be viewed as a back translation.
12
13 This tool is available from the Galaxy Tool Shed at:
14
15 * http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans
16
17 The underlying Python script can also be used outside of Galaxy, for
18 details run::
19
20 $ python align_back_trans.py
21
22 Automated Installation
23 ======================
24
25 This should be straightforward using the Galaxy Tool Shed, which should be
26 able to automatically install the dependency on Biopython, and then install
27 this tool and run its unit tests.
28
29
30 Manual Installation
31 ===================
32
33 There are just two files to install to use this tool from within Galaxy:
34
35 * ``align_back_trans.py`` (the Python script)
36 * ``align_back_trans.xml`` (the Galaxy tool definition)
37
38 The suggested location is in a dedicated ``tools/align_back_trans`` folder.
39
40 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
41 the tool. One suggested location is in the multiple alignments section. Simply
42 add the line::
43
44 <tool file="align_back_trans/align_back_trans.xml" />
45
46 You will also need to install Biopython 1.62 or later.
47
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
52
53 That's it.
54
55
56 History
57 =======
58
59 ======= ======================================================================
60 Version Changes
61 ------- ----------------------------------------------------------------------
62 v0.0.1 - Initial version, based on a previously written Python script
63 v0.0.2 - Optionally check the translation is consistent
64 v0.0.3 - First official release
65 v0.0.4 - Simplified XML to apply input format to output data.
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).
72 v0.0.7 - Minor Python code style improvements (internal change only).
73 ======= ======================================================================
74
75
76 Developers
77 ==========
78
79 This script was initially developed on this repository:
80 https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py
81
82 With the addition of a Galaxy wrapper, developement moved here:
83 https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
84
85 For pushing a release to the test or main "Galaxy Tool Shed", use the following
86 Planemo commands (which requires you have set your Tool Shed access details in
87 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
88
89 $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
90 ...
91
92 or::
93
94 $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
95 ...
96
97 To just build and check the tar ball, use::
98
99 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/align_back_trans/
100 ...
101 $ tar -tzf shed_upload.tar.gz
102 test-data/demo_nucs.fasta
103 test-data/demo_nucs_trailing_stop.fasta
104 test-data/demo_prot_align.fasta
105 test-data/demo_nuc_align.fasta
106 tools/align_back_trans/README.rst
107 tools/align_back_trans/align_back_trans.py
108 tools/align_back_trans/align_back_trans.xml
109 tools/align_back_trans/tool_dependencies.xml
110
111
112 Licence (MIT)
113 =============
114
115 Permission is hereby granted, free of charge, to any person obtaining a copy
116 of this software and associated documentation files (the "Software"), to deal
117 in the Software without restriction, including without limitation the rights
118 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
119 copies of the Software, and to permit persons to whom the Software is
120 furnished to do so, subject to the following conditions:
121
122 The above copyright notice and this permission notice shall be included in
123 all copies or substantial portions of the Software.
124
125 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
126 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
127 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
128 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
129 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
130 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
131 THE SOFTWARE.