Mercurial > repos > peterjc > blastxml_to_top_descr
annotate tools/blastxml_to_top_descr/README.rst @ 12:fe1ed74793c9 draft
Uploaded v0.1.1, embed citation in tool XML
author | peterjc |
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date | Wed, 30 Jul 2014 05:36:52 -0400 |
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11
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1 Galaxy tool to extract top BLAST hit descriptions from BLAST XML |
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2 ================================================================ |
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3 |
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4 This tool is copyright 2012-2013 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. |
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7 |
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8 This tool is a short Python script to parse a BLAST XML file, and extract the |
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9 identifiers with description for the top matches (by default the top 3), and |
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10 output these as a simple tabular file along with the query identifiers. |
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11 |
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12 It is available from the Galaxy Tool Shed at: |
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13 http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr |
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14 |
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15 This requires the 'blast_datatypes' repository from the Galaxy Tool Shed |
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16 to provide the 'blastxml' file format definition. |
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17 |
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18 |
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19 Automated Installation |
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20 ====================== |
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21 |
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22 This should be straightforward, Galaxy should automatically install the |
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23 'blast_datatypes' dependency. |
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24 |
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25 |
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26 Manual Installation |
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27 =================== |
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28 |
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29 If you haven't done so before, first install the 'blast_datatypes' repository. |
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30 |
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31 There are just two files to install (if doing this manually): |
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32 |
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33 * blastxml_to_top_descr.py (the Python script) |
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34 * blastxml_to_top_descr.xml (the Galaxy tool definition) |
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35 |
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36 The suggested location is in the Galaxy folder tools/ncbi_blast_plus next to |
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37 the NCBI BLAST+ tool wrappers. |
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38 |
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39 You will also need to modify the tools_conf.xml file to tell Galaxy to offer |
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40 the tool. e.g. next to the NCBI BLAST+ tools. Simply add the line:: |
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41 |
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42 <tool file="ncbi_blast_plus/blastxml_to_top_descr.xml" /> |
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43 |
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44 To run the tool's tests, also add this line to tools_conf.xml.sample then:: |
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45 |
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46 $ sh run_functional_tests.sh -id blastxml_to_top_descr |
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47 |
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48 |
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49 History |
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50 ======= |
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51 |
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52 ======= ====================================================================== |
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53 Version Changes |
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54 ------- ---------------------------------------------------------------------- |
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55 v0.0.1 - Initial version. |
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56 v0.0.2 - Since BLAST+ was moved out of the Galaxy core, now have a dependency |
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57 on the 'blast_datatypes' repository in the Tool Shed. |
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58 v0.0.3 - Include the test files required to run the unit tests |
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59 v0.0.4 - Quote filenames in case they contain spaces (internal change) |
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60 v0.0.5 - Include number of queries with BLAST matches in stdout (peek text) |
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61 v0.0.6 - Check for errors via the script's return code (internal change) |
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62 v0.0.7 - Link to Tool Shed added to help text and this documentation. |
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63 - Tweak dependency on blast_datatypes to also work on Test Tool Shed |
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64 - Adopt standard MIT License. |
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65 v0.0.8 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast |
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66 v0.0.9 - Updated citation information (Cock et al. 2013). |
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67 v0.0.10 - Update help text to mention BLAST+ 2.2.28 can produce tabular files |
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68 including the description/title (via the salltitles field). |
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69 v0.1.0 - Switch to using an optparse based API for Python script internally. |
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70 - Support BLAST XML with multiple ``<Iteration>`` blocks per query. |
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71 - Support the default 25 column extended tabular BLAST output. |
12 | 72 v0.1.1 - Embed citation information in the tool XML (new Galaxy feature). |
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73 ======= ====================================================================== |
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74 |
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75 |
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76 Bug Reports |
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77 =========== |
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78 |
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79 You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask |
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80 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev |
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81 |
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82 |
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83 Developers |
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84 ========== |
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85 |
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86 This script and related tools were originally developed on the 'tools' branch of |
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87 the following Mercurial repository: https://bitbucket.org/peterjc/galaxy-central/ |
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88 |
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89 As of July 2013, development is continuing on a dedicated GitHub repository: |
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90 https://github.com/peterjc/galaxy_blast |
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91 |
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92 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use |
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93 the following command from the GitHub repository root folder:: |
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94 |
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95 $ tar -czf blastxml_to_top_descr.tar.gz tools/blastxml_to_top_descr/README.rst tools/blastxml_to_top_descr/blastxml_to_top_descr.* tools/blastxml_to_top_descr/repository_dependencies.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_top3.tabular test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular |
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96 |
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97 Check this worked:: |
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98 |
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99 $ tar -tzf blastxml_to_top_descr.tar.gz |
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100 tools/blastxml_to_top_descr/README.rst |
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101 tools/blastxml_to_top_descr/blastxml_to_top_descr.py |
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102 tools/blastxml_to_top_descr/blastxml_to_top_descr.xml |
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103 tools/blastxml_to_top_descr/repository_dependencies.xml |
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104 test-data/blastp_four_human_vs_rhodopsin.xml |
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105 test-data/blastp_four_human_vs_rhodopsin_top3.tabular |
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106 test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular |
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107 test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular |
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108 |
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109 |
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110 Licence (MIT) |
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111 ============= |
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112 |
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113 Permission is hereby granted, free of charge, to any person obtaining a copy |
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114 of this software and associated documentation files (the "Software"), to deal |
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115 in the Software without restriction, including without limitation the rights |
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116 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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117 copies of the Software, and to permit persons to whom the Software is |
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118 furnished to do so, subject to the following conditions: |
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119 |
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120 The above copyright notice and this permission notice shall be included in |
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121 all copies or substantial portions of the Software. |
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122 |
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123 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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124 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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125 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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126 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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127 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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128 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
98f8431dab44
Uploaded v0.1.0, now also handles extended tabular BLAST output.
peterjc
parents:
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changeset
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129 THE SOFTWARE. |