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1 Galaxy tool to extract top BLAST hit descriptions from BLAST XML
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2 ================================================================
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3
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4 This tool is copyright 2012 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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11
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12 There are no additional dependancies.
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13
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14
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15 Manual Installation
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16 ===================
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17
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18 There are just two files to install (if doing this manually):
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19
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20 * blastxml_to_top_descr.py (the Python script)
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21 * blastxml_to_top_descr.xml (the Galaxy tool definition)
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22
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23 The suggested location is in the Galaxy folder tools/ncbi_blast_plus next to
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24 the NCBI BLAST+ tool wrappers.
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25
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26 You will also need to modify the tools_conf.xml file to tell Galaxy to offer
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27 the tool. e.g. next to the NCBI BLAST+ tools. Simply add the line:
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28
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29 <tool file="filters/seq_select_by_id.xml" />
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30
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31 To run the tool's tests, also add this line to tools_conf.xml.sample then:
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32
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33 $ sh run_functional_tests.sh -id blastxml_to_top_descr
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34
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35
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36 History
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37 =======
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38
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39 v0.0.1 - Initial version.
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40
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41
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42 Developers
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43 ==========
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44
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45 This script and related tools are being developed on the following hg branch:
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46 http://bitbucket.org/peterjc/galaxy-central/src/tools
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47
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48 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
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49 the following command from the Galaxy root folder:
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50
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51 $ tar -czf blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.*
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52
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53 Check this worked:
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54
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55 $ tar -tzf blastxml_to_top_descr.tar.gz
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56 tools/ncbi_blast_plus/blastxml_to_top_descr.py
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57 tools/ncbi_blast_plus/blastxml_to_top_descr.txt
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58 tools/ncbi_blast_plus/blastxml_to_top_descr.xml
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59
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60 Licence (MIT/BSD style)
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61 =======================
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62
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63 Permission to use, copy, modify, and distribute this software and its
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64 documentation with or without modifications and for any purpose and
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65 without fee is hereby granted, provided that any copyright notices
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66 appear in all copies and that both those copyright notices and this
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67 permission notice appear in supporting documentation, and that the
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68 names of the contributors or copyright holders not be used in
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69 advertising or publicity pertaining to distribution of the software
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70 without specific prior permission.
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71
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72 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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73 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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74 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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75 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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76 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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77 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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78 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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79 OR PERFORMANCE OF THIS SOFTWARE.
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