Mercurial > repos > peterjc > get_orfs_or_cdss
annotate tools/get_orfs_or_cdss/README.rst @ 12:71905a6d52a7 draft default tip
"Update all the pico_galaxy tools on main Tool Shed"
author | peterjc |
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date | Fri, 16 Apr 2021 22:37:04 +0000 |
parents | d51db443aaa4 |
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rev | line source |
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5 | 1 Galaxy tool to find ORFs or simple CDSs |
2 ======================================= | |
3 | |
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4 This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute |
5 | 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. |
8 | 6 Additions copyright 2015-2016 by Eric Rasche. |
5 | 7 See the licence text below (MIT licence). |
8 | |
9 This tool is a short Python script (using Biopython library functions) | |
10 to search nucleotide sequences for open reading frames (ORFs) or coding | |
11 sequences (CDSs) where the first potential start codon is used. See the | |
12 help text in the XML file for more information. | |
13 | |
14 This tool is available from the Galaxy Tool Shed at: | |
15 | |
16 * http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss | |
17 | |
18 See also the EMBOSS tool ``getorf`` which offers similar functionality and | |
19 has also been wrapped for use within Galaxy. | |
20 | |
21 | |
22 Automated Installation | |
23 ====================== | |
24 | |
25 This should be straightforward using the Galaxy Tool Shed, which should be | |
26 able to automatically install the dependency on Biopython, and then install | |
27 this tool and run its unit tests. | |
28 | |
29 | |
30 Manual Installation | |
31 =================== | |
32 | |
33 There are just two files to install to use this tool from within Galaxy: | |
34 | |
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35 * ``get_orfs_or_cdss.py`` (the Python script) |
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36 * ``get_orfs_or_cdss.xml`` (the Galaxy tool definition) |
5 | 37 |
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38 The suggested location is in a dedicated ``tools/get_orfs_or_cdss`` folder. |
5 | 39 |
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40 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the |
5 | 41 tool. One suggested location is in the filters section. Simply add the line:: |
42 | |
43 <tool file="get_orfs_or_cdss/get_orfs_or_cdss.xml" /> | |
44 | |
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45 You will also need to install Biopython 1.65 or later (slightly older versions |
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46 should be fine, but will not have the latest NCBI genetic code tables). |
5 | 47 |
10 | 48 If you wish to run the unit tests, also move/copy the ``test-data/`` files |
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49 under Galaxy's ``test-data/`` folder. Then:: |
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50 |
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51 ./run_tests.sh -id get_orfs_or_cdss |
5 | 52 |
53 That's it. | |
54 | |
55 | |
56 History | |
57 ======= | |
58 | |
59 ======= ====================================================================== | |
60 Version Changes | |
61 ------- ---------------------------------------------------------------------- | |
62 v0.0.1 - Initial version. | |
63 v0.0.2 - Correct labelling issue on reverse strand. | |
64 - Use the new <stdio> settings in the XML wrappers to catch errors | |
65 v0.0.3 - Include unit tests. | |
66 - Record Python script version when run from Galaxy. | |
67 v0.0.4 - Link to Tool Shed added to help text and this documentation. | |
68 v0.0.5 - Automated intallation of the Biopython dependency. | |
69 - Use reStructuredText for this README file. | |
70 - Adopt standard MIT License. | |
71 - Updated citation information (Cock et al. 2013). | |
72 - Renamed folder and adopted README.rst naming. | |
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73 v0.0.6 - Corrected automated dependency defintion. |
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74 v0.0.7 - Tool definition now embeds citation information. |
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75 v0.1.0 - Tool now outputs BED formatted calls (by @erasche, Eric Rasche). |
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76 - Using ``optparse`` for the Python command line API (Eric Rasche). |
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77 - Added NCBI genetic code table 24, Pterobranchia Mitochondrial. |
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78 v0.1.1 - Reorder XML elements (internal change only). |
8 | 79 v0.2.0 - Tool now also outputs GFF3 formatted calls (Eric Rasche). |
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80 v0.2.1 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. |
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81 - Added NCBI genetic code table 24, Candidate Division SR1 and |
10 | 82 Gracilibacteria. |
83 v0.2.2 - Use ``<command detect_errors="aggressive">`` (internal change only). | |
84 - Single quote command line arguments (internal change only). | |
11 | 85 v0.2.3 - Python 3 compatible print function. |
5 | 86 ======= ====================================================================== |
87 | |
88 | |
89 Developers | |
90 ========== | |
91 | |
92 This script and related tools were initially developed on the following hg branch: | |
93 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
94 | |
95 Development has now moved to a dedicated GitHub repository: | |
96 https://github.com/peterjc/pico_galaxy/tree/master/tools | |
97 | |
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98 For pushing a release to the test or main "Galaxy Tool Shed", use the following |
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99 Planemo commands (which requires you have set your Tool Shed access details in |
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100 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: |
5 | 101 |
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102 $ planemo shed_update -t testtoolshed --check_diff tools/get_orfs_or_cdss/ |
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103 ... |
5 | 104 |
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105 or:: |
5 | 106 |
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107 $ planemo shed_update -t toolshed --check_diff tools/get_orfs_or_cdss/ |
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108 ... |
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109 |
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110 To just build and check the tar ball, use:: |
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111 |
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112 $ planemo shed_upload --tar_only tools/get_orfs_or_cdss/ |
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113 ... |
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114 $ tar -tzf shed_upload.tar.gz |
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115 test-data/Ssuis.fasta |
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116 test-data/get_orf_input.Suis_ORF.bed |
5 | 117 test-data/get_orf_input.Suis_ORF.nuc.fasta |
118 test-data/get_orf_input.Suis_ORF.prot.fasta | |
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119 test-data/get_orf_input.fasta |
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120 test-data/get_orf_input.t11_bed_out.bed |
5 | 121 test-data/get_orf_input.t11_nuc_out.fasta |
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122 test-data/get_orf_input.t11_open_bed_out.bed |
5 | 123 test-data/get_orf_input.t11_open_nuc_out.fasta |
124 test-data/get_orf_input.t11_open_prot_out.fasta | |
125 test-data/get_orf_input.t11_prot_out.fasta | |
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126 test-data/get_orf_input.t1_bed_out.bed |
5 | 127 test-data/get_orf_input.t1_nuc_out.fasta |
128 test-data/get_orf_input.t1_prot_out.fasta | |
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129 tools/get_orfs_or_cdss/get_orfs_or_cdss.py |
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130 tools/get_orfs_or_cdss/get_orfs_or_cdss.xml |
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131 tools/get_orfs_or_cdss/README.rst |
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132 tools/get_orfs_or_cdss/tool_dependencies.xml |
5 | 133 |
134 | |
135 Licence (MIT) | |
136 ============= | |
137 | |
138 Permission is hereby granted, free of charge, to any person obtaining a copy | |
139 of this software and associated documentation files (the "Software"), to deal | |
140 in the Software without restriction, including without limitation the rights | |
141 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
142 copies of the Software, and to permit persons to whom the Software is | |
143 furnished to do so, subject to the following conditions: | |
144 | |
145 The above copyright notice and this permission notice shall be included in | |
146 all copies or substantial portions of the Software. | |
147 | |
148 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
149 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
150 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
151 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
152 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
153 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
154 THE SOFTWARE. |