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annotate tools/protein_analysis/effectiveT3.txt @ 0:096088373590

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Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 16:32:23 -0400
parents
children 7479dbb285b5
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096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
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1 Galaxy wrapper for EffectiveT3 v1.0.1
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2 =====================================
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3
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4 This wrapper is copyright 2011 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 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 http://dx.doi.org/10.1093/nar/gkq1154
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14
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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 http://dx.doi.org/10.1371/journal.ppat.1000376
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20 http://effectors.org/
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21
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22 You can change the path by editing the definition near the start of the Python
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23 script effectiveT3.py, but by default it expects the following files to be
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24 installed at these locations:
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26 /opt/EffectiveT3/TTSS_GUI-1.0.1.jar
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27 /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar
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28 /opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar
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29 /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar
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31 To install the wrapper copy or move the following files under the Galaxy tools
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32 folder, e.g. in a tools/protein_analysis folder:
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34 * effectiveT3.xml (the Galaxy tool definition)
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35 * effectiveT3.py (the Python wrapper script)
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36 * effectiveT3.txt (this README file)
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37
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38 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
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39 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
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40 it next to them. Just add the line:
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41
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42 <tool file="protein_analysis/effectiveT3.xml" />
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43
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44 That's it.
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47 History
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48 =======
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49
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50 v0.0.7 - Initial public release
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53 Developers
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54 ==========
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55
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56 This script and related tools are being developed on the following hg branch:
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57 http://bitbucket.org/peterjc/galaxy-central/src/tools
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58
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59 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
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60 the following command from the Galaxy root folder:
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61
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62 $ tar -czf effectiveT3.tar.gz tools/protein_analysis/effectiveT3.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt
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63
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64 Check this worked:
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65
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66 $ tar -tzf effectiveT3.tar.gz
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67 tools/protein_analysis/effectiveT3.xml
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68 tools/protein_analysis/effectiveT3.py
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69 tools/protein_analysis/effectiveT3.txt
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71
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72 Licence (MIT/BSD style)
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73 =======================
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74
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75 Permission to use, copy, modify, and distribute this software and its
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76 documentation with or without modifications and for any purpose and
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77 without fee is hereby granted, provided that any copyright notices
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78 appear in all copies and that both those copyright notices and this
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79 permission notice appear in supporting documentation, and that the
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80 names of the contributors or copyright holders not be used in
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81 advertising or publicity pertaining to distribution of the software
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82 without specific prior permission.
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83
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84 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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85 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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86 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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87 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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88 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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89 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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90 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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91 OR PERFORMANCE OF THIS SOFTWARE.
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92
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93 NOTE: This is the licence for the Galaxy Wrapper only. NLStradamus
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94 is available and licenced separately.