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planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/fastq_pair_names commit 1700cce8c849ef83cd593bc0ffc547bd4614636a
author peterjc
date Wed, 13 May 2015 05:03:55 -0400
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18:7440116e24e5 19:20eb53c8a79d
1 Galaxy tool to extract FASTQ paired read names
2 ==============================================
3
4 This tool is copyright 2014-2015 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 handles FASTQ files with paired
9 reads to identify pairs, and can be used to recover missing partners.
10
11 The inputs are FASTQ files, and the output is two tabular files. The first
12 file has one line per read pair (showing the read pair's name with any
13 suffix like ``/1`` or ``/2`` removed). The second file has one line per
14 non-paired read (or paired read with unrecognised naming) giving the read
15 name.
16
17 This tool is available from the Galaxy Tool Shed at:
18 http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_pair_names
19
20
21 Automated Installation
22 ======================
23
24 This should be straightforward, Galaxy should automatically download and install
25 the tool from the Galaxy Tool Shed, and run the unit tests.
26
27
28 Manual Installation
29 ===================
30
31 There are just two files to install:
32
33 * ``fastq_pair_names.py`` (the Python script)
34 * ``fastq_pair_names.xml`` (the Galaxy tool definition)
35
36 The suggested location is in the Galaxy folder tools/fastq next to other FASTQ
37 tools provided with Galaxy.
38
39 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
40 the tool. One suggested location is next to the ``fastq_filter.xml`` entry, or use
41 a dedicated folder like ``tools/fastq_pair_names``. Then simply add the line::
42
43 <tool file="fastq_pair_names/fastq_pair_names.xml" />
44
45 That's it.
46
47
48 History
49 =======
50
51 ======= ======================================================================
52 Version Changes
53 ------- ----------------------------------------------------------------------
54 v0.0.1 - Initial version.
55 v0.0.2 - Tool definition now embeds citation information.
56 v0.0.3 - Reorder XML elements (internal change only).
57 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
58 ======= ======================================================================
59
60
61 Developers
62 ==========
63
64 Development is on this GitHub repository:
65 https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names
66
67 For pushing a release to the test or main "Galaxy Tool Shed", use the following
68 Planemo commands (which requires you have set your Tool Shed access details in
69 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
70
71 $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/fastq_pair_names/
72 ...
73
74 or::
75
76 $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/fastq_pair_names/
77 ...
78
79 To just build and check the tar ball, use::
80
81 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/fastq_pair_names/
82 ...
83 $ tar -tzf shed_upload.tar.gz
84 test-data/empty_file.dat
85 test-data/sanger-pairs-mixed.fastq
86 test-data/sanger-pairs-names.tabular
87 tools/fastq_pair_names/README.rst
88 tools/fastq_pair_names/fastq_pair_names.py
89 tools/fastq_pair_names/fastq_pair_names.xml
90
91
92 Licence (MIT)
93 =============
94
95 Permission is hereby granted, free of charge, to any person obtaining a copy
96 of this software and associated documentation files (the "Software"), to deal
97 in the Software without restriction, including without limitation the rights
98 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
99 copies of the Software, and to permit persons to whom the Software is
100 furnished to do so, subject to the following conditions:
101
102 The above copyright notice and this permission notice shall be included in
103 all copies or substantial portions of the Software.
104
105 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
106 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
107 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
108 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
109 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
110 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
111 THE SOFTWARE.