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Migrated tool version 0.0.4 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 17:21:17 -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 by Peter Cock, SCRI, UK. All rights reserved.
5 See the licence text below.
6
7 This tool is a short Python script (using the Biopython library functions) which
8 divides a FASTQ file into paired reads, and single or orphan reads. You can have
9 separate files for the forward/reverse reads, or have them interleaved in a
10 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 There are just two files to install:
16
17 * fastq_paired_unpaired.py (the Python script)
18 * fastq_paired_unpaired.xml (the Galaxy tool definition)
19
20 The suggested location is in the Galaxy folder tools/fastq next to other FASTQ
21 tools provided with Galaxy.
22
23 You will also need to modify the tools_conf.xml file to tell Galaxy to offer
24 the tool. One suggested location is next to the fastq_filter.xml entry. Simply
25 add the line:
26
27 <tool file="fastq/fastq_paired_unpaired.xml" />
28
29 That's it.
30
31
32 History
33 =======
34
35 v0.0.1 - Initial version, using Biopython
36 v0.0.2 - Help text; cope with multiple pairs per template
37 v0.0.3 - Galaxy XML wrappers added
38 v0.0.4 - Use Galaxy library to handle FASTQ files (avoid Biopython dependency)
39
40
41 Developers
42 ==========
43
44 This script and other tools for filtering FASTA, FASTQ and SFF files are
45 currently being developed on the following hg branch:
46 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
47
48 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
49 the following command from the Galaxy root folder:
50
51 tar -czf fastq_paired_unpaired.tar.gz tools/fastq/fastq_paired_unpaired.*
52
53 Check this worked:
54
55 $ tar -tzf fastq_paired_unpaired.tar.gz
56 fastq/fastq_paired_unpaired.py
57 fastq/fastq_paired_unpaired.txt
58 fastq/fastq_paired_unpaired.xml
59
60
61 Licence (MIT/BSD style)
62 =======================
63
64 Permission to use, copy, modify, and distribute this software and its
65 documentation with or without modifications and for any purpose and
66 without fee is hereby granted, provided that any copyright notices
67 appear in all copies and that both those copyright notices and this
68 permission notice appear in supporting documentation, and that the
69 names of the contributors or copyright holders not be used in
70 advertising or publicity pertaining to distribution of the software
71 without specific prior permission.
72
73 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
74 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
75 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
76 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
77 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
78 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
79 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
80 OR PERFORMANCE OF THIS SOFTWARE.