Mercurial > repos > peterjc > venn_list

annotate tools/plotting/venn_list.txt @ 4:29fcd027d67a draft

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Uploaded v0.0.6 take 1, simple test (which currently fails)
author peterjc
date Thu, 16 May 2013 12:43:57 -0400
parents aefc86eda5f6
children 51fe47a5a803
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aefc86eda5f6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
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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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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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20
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21 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
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22 tool. The suggested location is in the "Graph/Display Data" section. Simply add
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23 the line:
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25 <tool file="plotting/venn_list.xml" />
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27 You will also need to install Biopython 1.54 or later, and the R/Bioconductor
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28 pacakge limma. You should already have rpy installed for other Galaxy tools.
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31 History
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32 =======
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33
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34 v0.0.3 - Initial public release.
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35 v0.0.4 - Ignore blank lines when loading IDs from tabular files
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36 v0.0.5 - Explicit Galaxy error handling of return codes
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37 v0.0.6 - Added unit tests.
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40 Developers
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41 ==========
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42
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43 This script and related tools are being developed on the following hg branch:
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44 http://bitbucket.org/peterjc/galaxy-central/src/tools
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45
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46 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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47 the following command from the Galaxy root folder:
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48
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49 tar -czf venn_list.tar.gz tools/plotting/venn_list.* test-data/venn_list1.pdf test-data/venn_list.tabular
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51 Check this worked:
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52
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53 $ tar -tzf venn_list.tar.gz
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54 tools/plotting/venn_list.py
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55 tools/plotting/venn_list.txt
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56 tools/plotting/venn_list.xml
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57 test-data/venn_list1.pdf
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58 test-data/venn_list.tabular
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60
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61 Licence (MIT/BSD style)
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62 =======================
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63
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64 Permission to use, copy, modify, and distribute this software and its
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65 documentation with or without modifications and for any purpose and
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66 without fee is hereby granted, provided that any copyright notices
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67 appear in all copies and that both those copyright notices and this
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68 permission notice appear in supporting documentation, and that the
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69 names of the contributors or copyright holders not be used in
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70 advertising or publicity pertaining to distribution of the software
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71 without specific prior permission.
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72
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73 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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74 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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75 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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76 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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77 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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78 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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79 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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80 OR PERFORMANCE OF THIS SOFTWARE.