Mercurial > repos > peterjc > fasta_filter_by_id
annotate tools/fasta_tools/fasta_filter_by_id.txt @ 1:5cd569750e85
Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:22:48 -0400 |
parents | 2e5f8ad1a096 |
children | 5b552b3005f2 |
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0
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1 Galaxy tool to filter FASTA sequences by ID |
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2 =========================================== |
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3 |
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4 This tool is copyright 2010 by Peter Cock, SCRI, UK. All rights reserved. |
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5 See the licence text below. |
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6 |
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7 This tool is a short Python script (using the Galaxy library functions) which |
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8 divides a FASTA file in two, those sequences with or without an ID present in |
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9 the specified column(s) of a tabular file. Example uses include filtering based |
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10 on search results from a tool like NCBI BLAST, TMHMM or SignalP. |
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11 |
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12 There are just two files to install: |
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13 |
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14 * fasta_filter_by_id.py (the Python script) |
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15 * fasta_filter_by_id.xml (the Galaxy tool definition) |
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16 |
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17 The suggested location is next to the similarly named fasta_filter_by_length.py |
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18 and fasta_filter_by_length.xml files which are included with Galaxy, i.e. |
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19 in the Galaxy folder tools/fasta_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 |
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22 the tool. The suggested location is next to the fasta_filter_by_length.xml |
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23 entry. Simply add the line: |
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24 |
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25 <tool file="fasta_tools/fasta_filter_by_id.xml" /> |
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26 |
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27 That's it. |
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28 |
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29 |
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30 History |
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31 ======= |
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32 |
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33 v0.0.1 - Initial version (not publicly released) |
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34 v0.0.2 - Allow both, just pos or just neg output files |
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35 v0.0.3 - Include FASTA in tool name |
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36 |
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37 Developers |
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38 ========== |
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39 |
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40 This script and similar versions for FASTQ and SFF files are currently being |
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41 developed on the following hg branch: |
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42 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter |
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43 |
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44 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use |
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45 the following command from the Galaxy root folder: |
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46 |
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47 tar -czf fasta_filter_by_id.tar.gz tools/fasta_tools/fasta_filter_by_id.* |
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48 |
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49 Check this worked: |
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50 |
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51 $ tar -tzf fasta_filter_by_id.tar.gz |
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52 fasta_tools/fasta_filter_by_id.py |
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53 fasta_tools/fasta_filter_by_id.txt |
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54 fasta_tools/fasta_filter_by_id.xml |
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55 |
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56 |
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57 Licence (MIT/BSD style) |
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58 ======================= |
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59 |
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60 Permission to use, copy, modify, and distribute this software and its |
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61 documentation with or without modifications and for any purpose and |
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62 without fee is hereby granted, provided that any copyright notices |
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63 appear in all copies and that both those copyright notices and this |
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64 permission notice appear in supporting documentation, and that the |
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65 names of the contributors or copyright holders not be used in |
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66 advertising or publicity pertaining to distribution of the software |
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67 without specific prior permission. |
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68 |
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69 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL |
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70 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED |
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71 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE |
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72 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT |
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73 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS |
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74 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE |
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75 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE |
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76 OR PERFORMANCE OF THIS SOFTWARE. |