Mercurial > repos > peterjc > seq_select_by_id
comparison tools/seq_select_by_id/README.rst @ 4:6842c0c7bc70 draft
Uploaded v0.0.7, depend on Biopython 1.62, tabs to spaces in XML
author | peterjc |
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date | Mon, 28 Oct 2013 05:21:45 -0400 |
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children | 1a83f5ab9e95 |
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1 Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID | |
2 =============================================================== | |
3 | |
4 This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute | |
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | |
6 See the licence text below. | |
7 | |
8 This tool is a short Python script (using Biopython library functions) to extract | |
9 sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given | |
10 by a column of a tabular file. The output order follows that of the tabular file, | |
11 and if there are duplicates in the tabular file, there will be duplicates in the | |
12 output sequence file. | |
13 | |
14 This tool is available from the Galaxy Tool Shed at: | |
15 | |
16 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id | |
17 | |
18 See also the sister tools to filter sequence files according to IDs from column(s) | |
19 of a tabular file (where the output order follows the sequence file, and any | |
20 duplicate IDs are ignored) and rename sequences: | |
21 | |
22 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id | |
23 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename | |
24 | |
25 | |
26 Automated Installation | |
27 ====================== | |
28 | |
29 This should be straightforward using the Galaxy Tool Shed, which should be | |
30 able to automatically install the dependency on Biopython, and then install | |
31 this tool and run its unit tests. | |
32 | |
33 | |
34 Manual Installation | |
35 =================== | |
36 | |
37 There are just two files to install to use this tool from within Galaxy: | |
38 | |
39 * seq_select_by_id.py (the Python script) | |
40 * seq_select_by_id.xml (the Galaxy tool definition) | |
41 | |
42 The suggested location is a dedicated tools/seq_select_by_id folder. | |
43 | |
44 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the | |
45 tool. One suggested location is in the filters section. Simply add the line:: | |
46 | |
47 <tool file="seq_select_by_id/seq_select_by_id.xml" /> | |
48 | |
49 If you wish to run the unit tests, also add this to tools_conf.xml.sample | |
50 and move/copy the test-data files under Galaxy's test-data folder. Then:: | |
51 | |
52 $ ./run_functional_tests.sh -id seq_select_by_id | |
53 | |
54 You will also need to install Biopython 1.54 or later. That's it. | |
55 | |
56 | |
57 History | |
58 ======= | |
59 | |
60 ======= ====================================================================== | |
61 Version Changes | |
62 ------- ---------------------------------------------------------------------- | |
63 v0.0.1 - Initial version. | |
64 v0.0.3 - Ignore blank lines in input. | |
65 v0.0.4 - Record script version when run from Galaxy. | |
66 - Basic unit test included. | |
67 v0.0.5 - Check for errors using Python script's return code. | |
68 v0.0.6 - Link to Tool Shed added to help text and this documentation. | |
69 - Automatic installation of Biopython dependency. | |
70 - Use reStructuredText for this README file. | |
71 - Adopt standard MIT License. | |
72 v0.0.7 - Updated citation information (Cock et al. 2013). | |
73 - Fixed Biopython dependency setup. | |
74 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy | |
75 - Renamed folder and adopted README.rst naming. | |
76 ======= ====================================================================== | |
77 | |
78 | |
79 Developers | |
80 ========== | |
81 | |
82 This script and related tools were initially developed on the following hg branch: | |
83 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
84 | |
85 Development has now moved to a dedicated GitHub repository: | |
86 https://github.com/peterjc/pico_galaxy/tree/master/tools | |
87 | |
88 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | |
89 the following command from the Galaxy root folder:: | |
90 | |
91 $ 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/repository_dependencies.xml test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular | |
92 | |
93 Check this worked:: | |
94 | |
95 $ tar -tzf seq_select_by_id.tar.gz | |
96 tools/seq_select_by_id/README.rst | |
97 tools/seq_select_by_id/seq_select_by_id.py | |
98 tools/seq_select_by_id/seq_select_by_id.xml | |
99 tools/seq_select_by_id/repository_dependencies.xml | |
100 test-data/k12_ten_proteins.fasta | |
101 test-data/k12_hypothetical.fasta | |
102 test-data/k12_hypothetical.tabular | |
103 | |
104 | |
105 Licence (MIT) | |
106 ============= | |
107 | |
108 Permission is hereby granted, free of charge, to any person obtaining a copy | |
109 of this software and associated documentation files (the "Software"), to deal | |
110 in the Software without restriction, including without limitation the rights | |
111 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
112 copies of the Software, and to permit persons to whom the Software is | |
113 furnished to do so, subject to the following conditions: | |
114 | |
115 The above copyright notice and this permission notice shall be included in | |
116 all copies or substantial portions of the Software. | |
117 | |
118 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
119 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
120 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
121 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
122 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
123 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
124 THE SOFTWARE. |