Mercurial > repos > peterjc > align_back_trans

annotate tools/align_back_trans/README.rst @ 6:b27388e5a0bb draft

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v0.0.10 removed unused reference to muscle format
author peterjc
date Mon, 21 Aug 2017 06:26:14 -0400
parents 2c32e8a8990f
children 883842b81796
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1 Galaxy tool to back-translate a protein alignment to nucleotides
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2 ================================================================
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3
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4 This tool is copyright 2012-2017 by Peter Cock, The James Hutton Institute
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5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
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6 See the licence text below (MIT licence).
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7
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8 This tool is a short Python script (using Biopython library functions) to
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9 load a protein alignment, and matching nucleotide FASTA file of unaligned
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10 sequences, which are threaded onto the protein alignment in order to produce
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11 a codon aware nucleotide alignment - which can be viewed as a back translation.
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13 This tool is available from the Galaxy Tool Shed at:
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14
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15 * http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans
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17 The underlying Python script can also be used outside of Galaxy, for
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18 details run::
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19
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20 $ python align_back_trans.py
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21
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22 Automated Installation
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23 ======================
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24
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25 This should be straightforward using the Galaxy Tool Shed, which should be
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26 able to automatically install the dependency on Biopython, and then install
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27 this tool and run its unit tests.
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30 Manual Installation
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31 ===================
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32
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33 There are just two files to install to use this tool from within Galaxy:
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34
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35 * ``align_back_trans.py`` (the Python script)
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36 * ``align_back_trans.xml`` (the Galaxy tool definition)
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37
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38 The suggested location is in a dedicated ``tools/align_back_trans`` folder.
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39
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40 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
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41 the tool. One suggested location is in the multiple alignments section. Simply
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42 add the line::
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43
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44 <tool file="align_back_trans/align_back_trans.xml" />
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45
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46 You will also need to install Biopython 1.62 or later.
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47
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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 align_back_trans
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52
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53 That's it.
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56 History
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57 =======
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58
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59 ======= ======================================================================
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60 Version Changes
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61 ------- ----------------------------------------------------------------------
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62 v0.0.1 - Initial version, based on a previously written Python script
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63 v0.0.2 - Optionally check the translation is consistent
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64 v0.0.3 - First official release
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65 v0.0.4 - Simplified XML to apply input format to output data.
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66 - Fixed error message when sequence length not a multiple of three.
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67 v0.0.5 - More explicit error messages when seqences lengths do not match.
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68 - Tool definition now embeds citation information.
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69 v0.0.6 - Reorder XML elements (internal change only).
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70 - Use ``format_source=...`` tag.
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71 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
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72 v0.0.7 - Minor Python code style improvements (internal change only).
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73 v0.0.8 - Python coding style change to avoid lamba (internal change only).
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74 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
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75 - Added two recent NCBI genetic code tables,
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76
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77 - Table 24, *Pterobranchia* Mitochondrial Code,
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78 - Table 25, Candidate Division SR1 and *Gracilibacteria*.
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79
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80 - Use ``<command detect_errors="aggressive">`` (internal change only).
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81 - Single quote command line arguments (internal change only).
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82 v0.0.9 - Python 3 compatible print function.
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83 v0.0.10 - Remove unused reference to ``muscle`` format in wrapper, reported by
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84 Björn Grüning (internal change only).
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85 ======= ======================================================================
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86
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87
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88 Developers
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89 ==========
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90
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91 This script was initially developed on this repository:
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92 https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py
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93
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94 With the addition of a Galaxy wrapper, developement moved here:
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95 https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
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96
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97 For pushing a release to the test or main "Galaxy Tool Shed", use the following
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98 Planemo commands (which requires you have set your Tool Shed access details in
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99 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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100
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101 $ planemo shed_update -t testtoolshed --check_diff tools/align_back_trans/
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102 ...
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103
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104 or::
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105
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106 $ planemo shed_update -t toolshed --check_diff tools/align_back_trans/
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107 ...
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108
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109 To just build and check the tar ball, use::
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110
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111 $ planemo shed_upload --tar_only tools/align_back_trans/
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112 ...
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113 $ tar -tzf shed_upload.tar.gz
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114 test-data/demo_nucs.fasta
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115 test-data/demo_nucs_trailing_stop.fasta
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116 test-data/demo_prot_align.fasta
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117 test-data/demo_nuc_align.fasta
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118 tools/align_back_trans/README.rst
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119 tools/align_back_trans/align_back_trans.py
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120 tools/align_back_trans/align_back_trans.xml
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121 tools/align_back_trans/tool_dependencies.xml
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122
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123
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124 Licence (MIT)
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125 =============
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126
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127 Permission is hereby granted, free of charge, to any person obtaining a copy
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128 of this software and associated documentation files (the "Software"), to deal
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129 in the Software without restriction, including without limitation the rights
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130 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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131 copies of the Software, and to permit persons to whom the Software is
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132 furnished to do so, subject to the following conditions:
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133
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134 The above copyright notice and this permission notice shall be included in
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135 all copies or substantial portions of the Software.
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136
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137 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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138 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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139 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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140 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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141 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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142 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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143 THE SOFTWARE.