Mercurial > repos > peterjc > venn_list

annotate tools/plotting/venn_list.rst @ 3:6aae6bc0802d draft

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Uploaded v0.0.6, basic unit test, MIT licence, RST README, citation information, development moved to GitHub
author peterjc
date Wed, 18 Sep 2013 06:19:51 -0400
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1 Galaxy tool to draw a Venn Diagram with up to 3 sets
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2 ====================================================
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3
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4 This tool 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 tool is a short Python script (using both the Galaxy and Biopython library
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9 functions) to extract ID lists from tabular, FASTA, FASTQ or SFF files to build
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10 sets, which are then drawn using the R limma package function vennDiagram
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11 (called from Python using rpy).
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12
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13 There are just two files to install:
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15 * venn_list.py (the Python script)
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16 * venn_list.xml (the Galaxy tool definition)
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17
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18 The suggested location is in the Galaxy folder tools/plotting next to other
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19 graph drawing tools.
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21 You will also need to install Biopython 1.54 or later, and the R/Bioconductor
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22 pacakge limma. You should already have rpy installed for other Galaxy tools.
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23
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24 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
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25 tool. The suggested location is in the "Graph/Display Data" section. Simply add
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26 the line::
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28 <tool file="plotting/venn_list.xml" />
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30 If you wish to run the unit tests, also add this to tools_conf.xml.sample and
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31 move/copy the test-data files under Galaxy's test-data folder. Then::
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33 ./run_functional_tests.sh -id venn_list
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36 History
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37 =======
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38
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39 ======= ======================================================================
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40 Version Changes
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41 ------- ----------------------------------------------------------------------
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42 v0.0.3 - Initial public release.
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43 v0.0.4 - Ignore blank lines when loading IDs from tabular files
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44 v0.0.5 - Explicit Galaxy error handling of return codes
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45 v0.0.6 - Added unit tests.
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46 - Use reStructuredText for this README file.
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47 - Adopt standard MIT licence.
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48 - Updated citation information (Cock et al. 2013).
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49 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
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50 ======= ======================================================================
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52
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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 Development has now moved to a dedicated GitHub repository:
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60 https://github.com/peterjc/pico_galaxy/tree/master/tools
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61
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62 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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63 the following command from the Galaxy root folder::
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64
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65 $ tar -czf venn_list.tar.gz tools/plotting/venn_list.* test-data/venn_list1.pdf test-data/venn_list.tabular test-data/rhodopsin_proteins.fasta
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66
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67 Check this worked::
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68
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69 $ tar -tzf venn_list.tar.gz
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70 tools/plotting/venn_list.py
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71 tools/plotting/venn_list.rst
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72 tools/plotting/venn_list.xml
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73 test-data/venn_list1.pdf
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74 test-data/venn_list.tabular
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75 test-data/rhodopsin_proteins.fasta
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77
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78 Licence (MIT)
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79 =============
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80
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81 Permission is hereby granted, free of charge, to any person obtaining a copy
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82 of this software and associated documentation files (the "Software"), to deal
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83 in the Software without restriction, including without limitation the rights
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84 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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85 copies of the Software, and to permit persons to whom the Software is
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86 furnished to do so, subject to the following conditions:
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87
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88 The above copyright notice and this permission notice shall be included in
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89 all copies or substantial portions of the Software.
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90
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91 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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92 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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93 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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94 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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95 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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96 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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97 THE SOFTWARE.