Mercurial > repos > peterjc > blastxml_to_top_descr

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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr commit 3ac00a9f99a93cbc8a6c136a302e7fbb17da8f71-dirty"
author peterjc
date Thu, 10 Sep 2020 14:00:38 +0000
parents c0c0a615d7cc
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1 OBGalaxy tool to extract top BLAST hit descriptions from BLAST XML
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2 ==================================================================
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4 This tool is copyright 2012-2015 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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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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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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19 Automated Installation
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20 ======================
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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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26 Manual Installation
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27 ===================
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29 If you haven't done so before, first install the ``blast_datatypes`` repository.
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31 There are just two files to install (if doing this manually):
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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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36 The suggested location is in the Galaxy folder ``tools/ncbi_blast_plus/``
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37 next to the NCBI BLAST+ tool wrappers.
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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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42 <tool file="ncbi_blast_plus/blastxml_to_top_descr.xml" />
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44 If you wish to run the unit tests, alsomove/copy the ``test-data/`` files
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45 under Galaxy's ``test-data/`` folder. Then::
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47 $ sh run_tests.sh -id blastxml_to_top_descr
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50 History
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51 =======
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52
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53 ======= ======================================================================
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54 Version Changes
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55 ------- ----------------------------------------------------------------------
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56 v0.0.1 - Initial version.
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57 v0.0.2 - Since BLAST+ was moved out of the Galaxy core, now have a dependency
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58 on the ``blast_datatypes`` repository in the Tool Shed.
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59 v0.0.3 - Include the test files required to run the unit tests
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60 v0.0.4 - Quote filenames in case they contain spaces (internal change)
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61 v0.0.5 - Include number of queries with BLAST matches in stdout (peek text)
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62 v0.0.6 - Check for errors via the script's return code (internal change)
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63 v0.0.7 - Link to Tool Shed added to help text and this documentation.
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64 - Tweak dependency on ``blast_datatypes`` to also work on Test Tool Shed
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65 - Adopt standard MIT License.
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66 v0.0.8 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
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67 v0.0.9 - Updated citation information (Cock et al. 2013).
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68 v0.0.10 - Update help text to mention BLAST+ 2.2.28 can produce tabular files
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69 including the description/title (via the salltitles field).
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70 v0.1.0 - Switch to using an optparse based API for Python script internally.
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71 - Support BLAST XML with multiple ``<Iteration>`` blocks per query.
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72 - Support the default 25 column extended tabular BLAST output.
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73 v0.1.1 - Embed citation information in the tool XML (new Galaxy feature).
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74 v0.1.2 - Reorder XML elements (internal change only).
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75 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
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76 - Use ``<command detect_errors="aggressive">`` (internal change only).
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77 - Single quote command line arguments (internal change only).
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78 - Python 3 compatible syntax.
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79 ======= ======================================================================
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82 Bug Reports
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83 ===========
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84
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85 You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask
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86 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
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89 Developers
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90 ==========
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92 This script and related tools were originally developed on the 'tools' branch of
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93 the following Mercurial repository: https://bitbucket.org/peterjc/galaxy-central/
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95 As of July 2013, development is continuing on a dedicated GitHub repository:
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96 https://github.com/peterjc/galaxy_blast
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97
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98 For pushing a release to the test or main "Galaxy Tool Shed", use the following
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99 Planemo commands (which requires you have set your Tool Shed access details in
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100 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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101
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102 $ planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blastxml_to_top_descr/
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103 ...
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105 or::
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106
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107 $ planemo shed_update -t toolshed --check_diff ~/repositories/galaxy_blast/tools/blastxml_to_top_descr/
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108 ...
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110 To just build and check the tar ball, use::
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111
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112 $ planemo shed_upload --tar_only ~/repositories/galaxy_blast/tools/blastxml_to_top_descr/
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113 ...
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114 $ tar -tzf shed_upload.tar.gz
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115 test-data/blastp_four_human_vs_rhodopsin.xml
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116 test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular
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117 test-data/blastp_four_human_vs_rhodopsin_top3.tabular
b46c041afbe4 planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/blastxml_to_top_descr commit 87df4063e559fe6a4db806a52d657404c2ad766c
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118 test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular
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119 tools/blastxml_to_top_descr/README.rst
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120 tools/blastxml_to_top_descr/blastxml_to_top_descr.py
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121 tools/blastxml_to_top_descr/blastxml_to_top_descr.xml
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122 tools/blastxml_to_top_descr/repository_dependencies.xml
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123
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124
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125 Licence (MIT)
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126 =============
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127
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128 Permission is hereby granted, free of charge, to any person obtaining a copy
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129 of this software and associated documentation files (the "Software"), to deal
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130 in the Software without restriction, including without limitation the rights
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131 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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132 copies of the Software, and to permit persons to whom the Software is
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133 furnished to do so, subject to the following conditions:
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134
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135 The above copyright notice and this permission notice shall be included in
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136 all copies or substantial portions of the Software.
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137
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138 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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139 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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140 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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141 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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142 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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143 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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144 THE SOFTWARE.