Mercurial > repos > peterjc > fastq_paired_unpaired
comparison tools/fastq_paired_unpaired/README.rst @ 4:09f9f0e29e47 draft
v0.0.6 use format_source; v0.0.5 error handling & citation
author | peterjc |
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date | Wed, 05 Aug 2015 11:06:38 -0400 |
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children | b38bbcbd458d |
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1 Galaxy tool to divide FASTQ files into paired and unpaired reads | |
2 ================================================================ | |
3 | |
4 This tool is copyright 2010-2015 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 which divides a FASTQ file into paired | |
9 reads, and single or orphan reads. You can have separate files for the | |
10 forward/reverse reads, or have them interleaved in a single file. | |
11 | |
12 Note that the FASTQ variant is unimportant (Sanger, Solexa, Illumina, or even | |
13 Color Space should all work equally well). | |
14 | |
15 This tool is available from the Galaxy Tool Shed at: | |
16 http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired | |
17 | |
18 | |
19 Automated Installation | |
20 ====================== | |
21 | |
22 This should be straightforward, Galaxy should automatically download and install | |
23 the tool from the Galaxy Tool Shed, and run the unit tests | |
24 | |
25 | |
26 Manual Installation | |
27 =================== | |
28 | |
29 There are just two files to install: | |
30 | |
31 * ``fastq_paired_unpaired.py`` (the Python script) | |
32 * ``fastq_paired_unpaired.xml`` (the Galaxy tool definition) | |
33 | |
34 The suggested location is in the Galaxy folder tools/fastq next to other FASTQ | |
35 tools provided with Galaxy. | |
36 | |
37 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer | |
38 the tool. One suggested location is next to the ``fastq_filter.xml`` entry, or use | |
39 a dedicated folder like ``tools/fastq_paired_unpaired``. Then simply add the line:: | |
40 | |
41 <tool file="fastq_paired_unpaired/fastq_paired_unpaired.xml" /> | |
42 | |
43 That's it. | |
44 | |
45 | |
46 History | |
47 ======= | |
48 | |
49 ======= ====================================================================== | |
50 Version Changes | |
51 ------- ---------------------------------------------------------------------- | |
52 v0.0.1 - Initial version, using Biopython | |
53 v0.0.2 - Help text; cope with multiple pairs per template | |
54 v0.0.3 - Galaxy XML wrappers added | |
55 v0.0.4 - Use Galaxy library to handle FASTQ files (avoid Biopython dependency) | |
56 v0.0.5 - Handle Illumina 1.8 style pair names | |
57 v0.0.6 - Record script version when run from Galaxy | |
58 - Added unit test (FASTQ file using Sanger naming) | |
59 v0.0.7 - Link to Tool Shed added to help text and this documentation. | |
60 v0.0.8 - Use reStructuredText for this README file. | |
61 - Adopt standard MIT License. | |
62 - Updated citation information (Cock et al. 2013). | |
63 - Development moved to GitHub. | |
64 v0.0.9 - Renamed folder and adopted README.rst naming. | |
65 - Removed some unused code in the Python script. | |
66 v0.1.0 - Switch to using Biopython (easier to use script outside of Galaxy). | |
67 - Leaves FASTQ plus lines blank (smaller output files). | |
68 - Tool definition now embeds citation information. | |
69 v0.1.1 - Reorder XML elements (internal change only). | |
70 - Use ``format_source=...`` tag. | |
71 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). | |
72 ======= ====================================================================== | |
73 | |
74 | |
75 Developers | |
76 ========== | |
77 | |
78 This script and other tools for filtering FASTA, FASTQ and SFF files were | |
79 initially developed on the following hg branch: | |
80 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter | |
81 | |
82 Development has now moved to a dedicated GitHub repository: | |
83 https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired | |
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 --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/fastq_paired_unpaired/ | |
90 ... | |
91 | |
92 or:: | |
93 | |
94 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/fastq_paired_unpaired/ | |
95 ... | |
96 | |
97 To just build and check the tar ball, use:: | |
98 | |
99 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/fastq_paired_unpaired/ | |
100 ... | |
101 $ tar -tzf shed_upload.tar.gz | |
102 test-data/sanger-pairs-forward.fastq | |
103 test-data/sanger-pairs-interleaved.fastq | |
104 test-data/sanger-pairs-mixed.fastq | |
105 test-data/sanger-pairs-reverse.fastq | |
106 test-data/sanger-pairs-singles.fastq | |
107 tools/fastq_paired_unpaired/README.rst | |
108 tools/fastq_paired_unpaired/fastq_paired_unpaired.py | |
109 tools/fastq_paired_unpaired/fastq_paired_unpaired.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. |