Mercurial > repos > peterjc > get_orfs_or_cdss

comparison tools/get_orfs_or_cdss/README.rst @ 8:09a8be9247ca draft

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v0.2.0 with GFF3 output
author peterjc
date Sat, 09 Jan 2016 23:42:32 -0500
parents 705a2e2df7fb
children a06ad07431ba
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7:705a2e2df7fb 8:09a8be9247ca
1 Galaxy tool to find ORFs or simple CDSs 1 Galaxy tool to find ORFs or simple CDSs
2 ======================================= 2 =======================================
3 3
4 This tool is copyright 2011-2015 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 Additions copyright 2015-2016 by Eric Rasche.
6 See the licence text below (MIT licence). 7 See the licence text below (MIT licence).
7 8
8 This tool is a short Python script (using Biopython library functions) 9 This tool is a short Python script (using Biopython library functions)
9 to search nucleotide sequences for open reading frames (ORFs) or coding 10 to search nucleotide sequences for open reading frames (ORFs) or coding
10 sequences (CDSs) where the first potential start codon is used. See the 11 sequences (CDSs) where the first potential start codon is used. See the
73 v0.0.7 - Tool definition now embeds citation information. 74 v0.0.7 - Tool definition now embeds citation information.
74 v0.1.0 - Tool now outputs BED formatted calls (by @erasche, Eric Rasche). 75 v0.1.0 - Tool now outputs BED formatted calls (by @erasche, Eric Rasche).
75 - Using ``optparse`` for the Python command line API (Eric Rasche). 76 - Using ``optparse`` for the Python command line API (Eric Rasche).
76 - Added NCBI genetic code table 24, Pterobranchia Mitochondrial. 77 - Added NCBI genetic code table 24, Pterobranchia Mitochondrial.
77 v0.1.1 - Reorder XML elements (internal change only). 78 v0.1.1 - Reorder XML elements (internal change only).
79 v0.2.0 - Tool now also outputs GFF3 formatted calls (Eric Rasche).
78 ======= ====================================================================== 80 ======= ======================================================================
79 81
80 82
81 Developers 83 Developers
82 ========== 84 ==========
89 91
90 For pushing a release to the test or main "Galaxy Tool Shed", use the following 92 For pushing a release to the test or main "Galaxy Tool Shed", use the following
91 Planemo commands (which requires you have set your Tool Shed access details in 93 Planemo commands (which requires you have set your Tool Shed access details in
92 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: 94 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
93 95
94 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/ 96 $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/
95 ... 97 ...
96 98
97 or:: 99 or::
98 100
99 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/ 101 $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/
100 ... 102 ...
101 103
102 To just build and check the tar ball, use:: 104 To just build and check the tar ball, use::
103 105
104 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/ 106 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/