Mercurial > repos > peterjc > seq_rename
comparison tools/filters/seq_rename.txt @ 0:a4b9836f8f47
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:43:26 -0400 |
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children | 9c8c5079c8af |
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1 Galaxy tool to renamed FASTA, QUAL, FASTQ or SFF sequences | |
2 ========================================================== | |
3 | |
4 This tool is copyright 2011 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 rename | |
9 sequences from a FASTA, QUAL, FASTQ, or SFF file based on an ID mapping gives as | |
10 two columns of a tabular file. The output order follows that of the sequence file, | |
11 and if there are duplicates in the input sequence file, there will be duplicates | |
12 in the output sequence file. | |
13 | |
14 See also the sister tools to filter or select sequence files according to IDs | |
15 from column(s) of tabular file. | |
16 | |
17 | |
18 There are just two files to install: | |
19 | |
20 * seq_rename.py (the Python script) | |
21 * seq_rename.xml (the Galaxy tool definition) | |
22 | |
23 The suggested location is in the Galaxy folder tools/filters next to the tool | |
24 for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL. | |
25 | |
26 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the | |
27 tool. One suggested location is in the filters section. Simply add the line: | |
28 | |
29 <tool file="filters/seq_rename.xml" /> | |
30 | |
31 You will also need to install Biopython 1.54 or later. That's it. | |
32 | |
33 | |
34 History | |
35 ======= | |
36 | |
37 v0.0.1 - Initial version. | |
38 | |
39 | |
40 Developers | |
41 ========== | |
42 | |
43 This script and related tools are being developed on the following hg branch: | |
44 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
45 | |
46 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use | |
47 the following command from the Galaxy root folder: | |
48 | |
49 tar -czf seq_rename.tar.gz tools/filters/seq_rename.* | |
50 | |
51 Check this worked: | |
52 | |
53 $ tar -tzf seq_rename.tar.gz | |
54 filter/seq_rename.py | |
55 filter/seq_rename.txt | |
56 filter/seq_rename.xml | |
57 | |
58 | |
59 Licence (MIT/BSD style) | |
60 ======================= | |
61 | |
62 Permission to use, copy, modify, and distribute this software and its | |
63 documentation with or without modifications and for any purpose and | |
64 without fee is hereby granted, provided that any copyright notices | |
65 appear in all copies and that both those copyright notices and this | |
66 permission notice appear in supporting documentation, and that the | |
67 names of the contributors or copyright holders not be used in | |
68 advertising or publicity pertaining to distribution of the software | |
69 without specific prior permission. | |
70 | |
71 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
72 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
73 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
74 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
75 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
76 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
77 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
78 OR PERFORMANCE OF THIS SOFTWARE. |