Mercurial > repos > peterjc > get_orfs_or_cdss
comparison tools/fastq/fastq_paired_unpaired.rst @ 3:6a14074bc810 draft
Uploaded v0.0.8, automated Biopython dependency handling via ToolShed; MIT license; reST markup for README file.
author | peterjc |
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date | Mon, 29 Jul 2013 09:28:55 -0400 |
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1 Galaxy tool to divide FASTQ files into paired and unpaired reads | |
2 ================================================================ | |
3 | |
4 This tool is copyright 2010-2013 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 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. Simply | |
39 add the line:: | |
40 | |
41 <tool file="fastq/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 ======= ====================================================================== | |
63 | |
64 | |
65 Developers | |
66 ========== | |
67 | |
68 This script and other tools for filtering FASTA, FASTQ and SFF files are | |
69 currently being developed on the following hg branch: | |
70 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter | |
71 | |
72 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | |
73 the following command from the Galaxy root folder:: | |
74 | |
75 $ tar -czf fastq_paired_unpaired.tar.gz tools/fastq/fastq_paired_unpaired.* test-data/sanger-pairs-*.fastq | |
76 | |
77 Check this worked:: | |
78 | |
79 $ tar -tzf fastq_paired_unpaired.tar.gz | |
80 tools/fastq/fastq_paired_unpaired.py | |
81 tools/fastq/fastq_paired_unpaired.rst | |
82 tools/fastq/fastq_paired_unpaired.xml | |
83 test-data/sanger-pairs-forward.fastq | |
84 test-data/sanger-pairs-interleaved.fastq | |
85 test-data/sanger-pairs-mixed.fastq | |
86 test-data/sanger-pairs-reverse.fastq | |
87 test-data/sanger-pairs-singles.fastq | |
88 | |
89 | |
90 Licence (MIT) | |
91 ============= | |
92 | |
93 Permission is hereby granted, free of charge, to any person obtaining a copy | |
94 of this software and associated documentation files (the "Software"), to deal | |
95 in the Software without restriction, including without limitation the rights | |
96 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
97 copies of the Software, and to permit persons to whom the Software is | |
98 furnished to do so, subject to the following conditions: | |
99 | |
100 The above copyright notice and this permission notice shall be included in | |
101 all copies or substantial portions of the Software. | |
102 | |
103 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
104 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
105 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
106 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
107 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
108 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
109 THE SOFTWARE. |