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v0.0.11; more tests and assorting minor changes
author peterjc
date Wed, 13 May 2015 10:56:29 -0400
parents 1a83f5ab9e95
children a5602454b0ad
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5:1a83f5ab9e95 6:91f55ee8fea5
1 Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID 1 Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID
2 =============================================================== 2 ===============================================================
3 3
4 This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute 4 This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below. 6 See the licence text below.
7 7
8 This tool is a short Python script (using Biopython library functions) to extract 8 This tool is a short Python script (using Biopython library functions) to extract
9 sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given 9 sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given
34 Manual Installation 34 Manual Installation
35 =================== 35 ===================
36 36
37 There are just two files to install to use this tool from within Galaxy: 37 There are just two files to install to use this tool from within Galaxy:
38 38
39 * seq_select_by_id.py (the Python script) 39 * ``seq_select_by_id.py`` (the Python script)
40 * seq_select_by_id.xml (the Galaxy tool definition) 40 * ``seq_select_by_id.xml`` (the Galaxy tool definition)
41 41
42 The suggested location is a dedicated tools/seq_select_by_id folder. 42 The suggested location is a dedicated ``tools/seq_select_by_id`` folder.
43 43
44 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the 44 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
45 tool. One suggested location is in the filters section. Simply add the line:: 45 tool. One suggested location is in the filters section. Simply add the line::
46 46
47 <tool file="seq_select_by_id/seq_select_by_id.xml" /> 47 <tool file="seq_select_by_id/seq_select_by_id.xml" />
48 48
49 If you wish to run the unit tests, also add this to tools_conf.xml.sample 49 If you wish to run the unit tests, also move/copy the ``test-data/`` files
50 and move/copy the test-data files under Galaxy's test-data folder. Then:: 50 under Galaxy's ``test-data/`` folder. Then::
51 51
52 $ ./run_functional_tests.sh -id seq_select_by_id 52 $ ./run_tests.sh -id seq_select_by_id
53 53
54 You will also need to install Biopython 1.54 or later. That's it. 54 You will also need to install Biopython 1.54 or later. That's it.
55 55
56 56
57 History 57 History
71 - Adopt standard MIT License. 71 - Adopt standard MIT License.
72 v0.0.7 - Updated citation information (Cock et al. 2013). 72 v0.0.7 - Updated citation information (Cock et al. 2013).
73 - Fixed Biopython dependency setup. 73 - Fixed Biopython dependency setup.
74 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy 74 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
75 - Renamed folder and adopted README.rst naming. 75 - Renamed folder and adopted README.rst naming.
76 v0.0.8 - Corrected automated dependency definition 76 v0.0.8 - Corrected automated dependency definition.
77 v0.0.9 - Simplified XML to apply input format to output data.
78 - Tool definition now embeds citation information.
79 - Include input dataset name in output dataset names.
80 - If white space is found in the requested tabular field then only
81 the first word is used as the identifier (with a warning to stderr).
82 v0.0.10 - Includes testing of stdout messages.
83 - Includes testing of failure modes.
84 v0.0.11 - Use the ``format_source=...`` tag.
85 - Reorder XML elements (internal change only).
86 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
87 - Quote filenames in case of spaces (internal change only).
77 ======= ====================================================================== 88 ======= ======================================================================
78 89
79 90
80 Developers 91 Developers
81 ========== 92 ==========
84 http://bitbucket.org/peterjc/galaxy-central/src/tools 95 http://bitbucket.org/peterjc/galaxy-central/src/tools
85 96
86 Development has now moved to a dedicated GitHub repository: 97 Development has now moved to a dedicated GitHub repository:
87 https://github.com/peterjc/pico_galaxy/tree/master/tools 98 https://github.com/peterjc/pico_galaxy/tree/master/tools
88 99
89 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use 100 For pushing a release to the test or main "Galaxy Tool Shed", use the following
90 the following command from the Galaxy root folder:: 101 Planemo commands (which requires you have set your Tool Shed access details in
102 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
91 103
92 $ tar -czf seq_select_by_id.tar.gz tools/seq_select_by_id/README.rst tools/seq_select_by_id/seq_select_by_id.* tools/seq_select_by_id/tool_dependencies.xml test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular 104 $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_select_by_id/
105 ...
93 106
94 Check this worked:: 107 or::
95 108
96 $ tar -tzf seq_select_by_id.tar.gz 109 $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_select_by_id/
110 ...
111
112 To just build and check the tar ball, use::
113
114 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/seq_select_by_id/
115 ...
116 $ tar -tzf shed_upload.tar.gz
117 test-data/k12_hypothetical.fasta
118 test-data/k12_hypothetical.tabular
119 test-data/k12_hypothetical_alt.tabular
120 test-data/k12_ten_proteins.fasta
97 tools/seq_select_by_id/README.rst 121 tools/seq_select_by_id/README.rst
98 tools/seq_select_by_id/seq_select_by_id.py 122 tools/seq_select_by_id/seq_select_by_id.py
99 tools/seq_select_by_id/seq_select_by_id.xml 123 tools/seq_select_by_id/seq_select_by_id.xml
100 tools/seq_select_by_id/tool_dependencies.xml 124 tools/seq_select_by_id/tool_dependencies.xml
101 test-data/k12_ten_proteins.fasta
102 test-data/k12_hypothetical.fasta
103 test-data/k12_hypothetical.tabular
104 125
105 126
106 Licence (MIT) 127 Licence (MIT)
107 ============= 128 =============
108 129