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v0.0.21 - Added bio.tools xref
author peterjc
date Tue, 12 Mar 2024 16:04:13 +0000
parents a46d7861c32c
children
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1 Galaxy wrapper for EffectiveT3 v1.0.1
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2 =====================================
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4 This wrapper is copyright 2011-2017 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.
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8 This is a wrapper for the command line Java tool EffectiveT3, v1.0.1,
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9
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10 Jehl, Arnold and Rattei.
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11 Effective - a database of predicted secreted bacterial proteins
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12 Nucleic Acids Research, 39(Database issue), D591-5, 2011.
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13 https://doi.org/10.1093/nar/gkq1154
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15 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei.
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16 Sequence-based prediction of type III secreted proteins.
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17 PLoS Pathog. 5(4):e1000376, 2009.
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18 https://doi.org/10.1371/journal.ppat.1000376
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20 http://effectors.org/
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22 This wrapper is available from the Galaxy Tool Shed at:
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23 http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
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26 Automated Installation
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27 ======================
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29 This should be straightforward, Galaxy should automatically download and install
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30 the Jar files for effectiveT3 v1.0.1 and its associated models (animal, plant and
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31 standard).
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34 Manual Installation
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35 ===================
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36
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37 You can change the path by setting the environment variable ``$EFFECTIVET3`` to the
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38 relevant folder, but by default it expects the following files to be installed
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39 at these locations::
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41 /opt/EffectiveT3/TTSS_GUI-1.0.1.jar
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42 /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar
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43 /opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar
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44 /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar
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46 To install the wrapper copy or move the following files under the Galaxy tools
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47 folder, e.g. in a tools/effectiveT3 folder:
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48
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49 * ``effectiveT3.xml`` (the Galaxy tool definition)
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50 * ``effectiveT3.py`` (the Python wrapper script)
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51 * ``README.rst`` (this file)
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53 Also copy ``effectiveT3.loc.sample`` to ``effectiveT3.loc`` in the ``tool-data``
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54 folder (and edit if appropriate, e.g. to add or remove a model).
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56 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
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57 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
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58 it next to them. Just add the line::
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60 <tool file="effectiveT3/effectiveT3.xml" />
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62 If you wish to run the unit tests, also move/copy the ``test-data/`` files
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63 under Galaxy's ``test-data/`` folder. Then::
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65 $ ./run_tests.sh -id effectiveT3
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66
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67 That's it.
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70 History
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71 =======
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73 ======= ======================================================================
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74 Version Changes
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75 ------- ----------------------------------------------------------------------
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76 v0.0.7 - Initial public release
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77 v0.0.8 - Include ``effectiveT3.loc.sample`` in Tool Shed
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78 v0.0.9 - Check the return code for errors in the XML
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79 v0.0.10 - Added unit test
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80 v0.0.11 - Automated installation
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81 - Record version of Python script when called from Galaxy
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82 - Link to Tool Shed added to help text and this documentation.
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83 v0.0.12 - More explicit naming of the output dataset.
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84 - Adopt standard MIT licence.
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85 - Use reStructuredText for this README file.
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86 - Updated citation information (Cock et al. 2013).
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87 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
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88 v0.0.13 - Relax unit test to allow for small floating point score difference.
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89 - Tool definition now embeds citation information.
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90 v0.0.14 - Fixed error handling in ``effectiveT3.py``.
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91 v0.0.15 - Reorder XML elements (internal change only).
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92 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
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93 v0.0.16 - Updated URLs to download the tool and models.
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94 - Includes new standard classification model v2.0.2 (Sep 2015)
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95 as the default entry in ``tool-data/effectiveT3.loc``
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96 - Catch java exception, e.g. if Java too old for ``TTSS-STD-2.0.1.jar``
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97 v0.0.17 - Update tool dependency definition to use cached URL.
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98 - Minor internal changes to Python script for error reporting & style.
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99 v0.0.18 - Use ``<command detect_errors="aggressive">`` (internal change only).
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100 - Single quote command line arguments (internal change only).
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101 v0.0.19 - Python 3 compatible exception handling.
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102 v0.0.20 - Work with Effective T3 as installed by BioConda (which provides a
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103 wrapper script which can be used to find the main JAR file folder).
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104 v0.0.21 - Added bio.tools xref
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105 ======= ======================================================================
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107
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108 Developers
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109 ==========
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110
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111 This script and related tools were initially developed on the following hg branch:
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112 http://bitbucket.org/peterjc/galaxy-central/src/tools
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113
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114 Development has now moved to a dedicated GitHub repository:
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115 https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3
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116
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117 For pushing a release to the test or main "Galaxy Tool Shed", use the following
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118 Planemo commands (which requires you have set your Tool Shed access details in
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119 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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120
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121 $ planemo shed_update -t testtoolshed --check_diff tools/effectiveT3/
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122 ...
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124 or::
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125
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126 $ planemo shed_update -t toolshed --check_diff tools/effectiveT3/
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127 ...
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128
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129 To just build and check the tar ball, use::
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130
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131 $ planemo shed_upload --tar_only tools/effectiveT3/
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132 ...
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133 $ tar -tzf shed_upload.tar.gz
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134 tool-data/effectiveT3.loc.sample
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135 test-data/empty.fasta
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136 test-data/empty_effectiveT3.tabular
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137 test-data/four_human_proteins.fasta
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138 test-data/four_human_proteins.effectiveT3.tabular
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139 tool-data/effectiveT3.loc.sample
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140 tools/effectiveT3/README.rst
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141 tools/effectiveT3/effectiveT3.py
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142 tools/effectiveT3/effectiveT3.xml
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143 tools/effectiveT3/tool_dependencies.xml
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144
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145
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146 Licence (MIT)
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147 =============
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148
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149 Permission is hereby granted, free of charge, to any person obtaining a copy
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150 of this software and associated documentation files (the "Software"), to deal
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151 in the Software without restriction, including without limitation the rights
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152 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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153 copies of the Software, and to permit persons to whom the Software is
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154 furnished to do so, subject to the following conditions:
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155
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156 The above copyright notice and this permission notice shall be included in
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157 all copies or substantial portions of the Software.
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158
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159 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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160 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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161 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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162 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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163 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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164 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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165 THE SOFTWARE.
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166
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167 NOTE: This is the licence for the Galaxy Wrapper only.
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168 EffectiveT3 is available and licenced separately.