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comparison tools/get_orfs_or_cdss/README.rst @ 10:01b0488d9cfb draft

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v0.2.2 Internal changes to command line handling
author peterjc
date Tue, 16 May 2017 09:11:27 -0400
parents a06ad07431ba
children d51db443aaa4
comparison
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9:a06ad07431ba 10:01b0488d9cfb
43 <tool file="get_orfs_or_cdss/get_orfs_or_cdss.xml" /> 43 <tool file="get_orfs_or_cdss/get_orfs_or_cdss.xml" />
44 44
45 You will also need to install Biopython 1.65 or later (slightly older versions 45 You will also need to install Biopython 1.65 or later (slightly older versions
46 should be fine, but will not have the latest NCBI genetic code tables). 46 should be fine, but will not have the latest NCBI genetic code tables).
47 47
48 If you wish to run the unit tests, also move/copy the ``test-data/`` files 48 If you wish to run the unit tests, also move/copy the ``test-data/`` files
49 under Galaxy's ``test-data/`` folder. Then:: 49 under Galaxy's ``test-data/`` folder. Then::
50 50
51 ./run_tests.sh -id get_orfs_or_cdss 51 ./run_tests.sh -id get_orfs_or_cdss
52 52
53 That's it. 53 That's it.
77 - Added NCBI genetic code table 24, Pterobranchia Mitochondrial. 77 - Added NCBI genetic code table 24, Pterobranchia Mitochondrial.
78 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). 79 v0.2.0 - Tool now also outputs GFF3 formatted calls (Eric Rasche).
80 v0.2.1 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. 80 v0.2.1 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
81 - Added NCBI genetic code table 24, Candidate Division SR1 and 81 - Added NCBI genetic code table 24, Candidate Division SR1 and
82 Gracilibacteria. 82 Gracilibacteria.
83 v0.2.2 - Use ``<command detect_errors="aggressive">`` (internal change only).
84 - Single quote command line arguments (internal change only).
83 ======= ====================================================================== 85 ======= ======================================================================
84 86
85 87
86 Developers 88 Developers
87 ========== 89 ==========