# HG changeset patch # User jasper # Date 1486144263 18000 # Node ID bedf9f58c02550404f596142f34f9c9d601a1521 # Parent f2e2a5cf89116dac668f9363d79441615fba0f6c Uploaded diff -r f2e2a5cf8911 -r bedf9f58c025 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Feb 03 12:51:03 2017 -0500 @@ -0,0 +1,130 @@ +Galaxy tool to back-translate a protein alignment to nucleotides +================================================================ + +This tool is copyright 2012-2015 by Peter Cock, The James Hutton Institute +(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. +See the licence text below (MIT licence). + +This tool is a short Python script (using Biopython library functions) to +load a protein alignment, and matching nucleotide FASTA file of unaligned +sequences, which are threaded onto the protein alignment in order to produce +a codon aware nucleotide alignment - which can be viewed as a back translation. + +This tool is available from the Galaxy Tool Shed at: + +* http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans + +The underlying Python script can also be used outside of Galaxy, for +details run:: + + $ python align_back_trans.py + +Automated Installation +====================== + +This should be straightforward using the Galaxy Tool Shed, which should be +able to automatically install the dependency on Biopython, and then install +this tool and run its unit tests. + + +Manual Installation +=================== + +There are just two files to install to use this tool from within Galaxy: + +* ``align_back_trans.py`` (the Python script) +* ``align_back_trans.xml`` (the Galaxy tool definition) + +The suggested location is in a dedicated ``tools/align_back_trans`` folder. + +You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer +the tool. One suggested location is in the multiple alignments section. Simply +add the line:: + + + +You will also need to install Biopython 1.62 or later. + +If you wish to run the unit tests, also move/copy the ``test-data/`` files +under Galaxy's ``test-data/`` folder. Then:: + + ./run_tests.sh -id align_back_trans + +That's it. + + +History +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +v0.0.1 - Initial version, based on a previously written Python script +v0.0.2 - Optionally check the translation is consistent +v0.0.3 - First official release +v0.0.4 - Simplified XML to apply input format to output data. + - Fixed error message when sequence length not a multiple of three. +v0.0.5 - More explicit error messages when seqences lengths do not match. + - Tool definition now embeds citation information. +v0.0.6 - Reorder XML elements (internal change only). + - Use ``format_source=...`` tag. + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). +======= ====================================================================== + + +Developers +========== + +This script was initially developed on this repository: +https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py + +With the addition of a Galaxy wrapper, developement moved here: +https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans + +For pushing a release to the test or main "Galaxy Tool Shed", use the following +Planemo commands (which requires you have set your Tool Shed access details in +``~/.planemo.yml`` and that you have access rights on the Tool Shed):: + + $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/ + ... + +or:: + + $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/ + ... + +To just build and check the tar ball, use:: + + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/align_back_trans/ + ... + $ tar -tzf shed_upload.tar.gz + test-data/demo_nucs.fasta + test-data/demo_nucs_trailing_stop.fasta + test-data/demo_prot_align.fasta + test-data/demo_nuc_align.fasta + tools/align_back_trans/README.rst + tools/align_back_trans/align_back_trans.py + tools/align_back_trans/align_back_trans.xml + tools/align_back_trans/tool_dependencies.xml + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE.