Mercurial > repos > peterjc > fastq_filter_by_id
annotate tools/fastq/fastq_filter_by_id.txt @ 2:d570cc324779
Migrated tool version 0.0.4 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:24:08 -0400 |
parents | 10e963c79a45 |
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Migrated tool version 0.0.4 from old tool shed archive to new tool shed repository
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1 Obsolete |
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2 ======== |
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3 |
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4 This tool is now obsolete, having been replaced by a more general version |
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5 covering the FASTA, FASTQ and SFF sequence formats in a single tool. You |
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6 should only install this tool if you need to support existing workflows |
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7 which used it. |
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8 |
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9 Galaxy tool to filter FASTQ sequences by ID |
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10 =========================================== |
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11 |
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12 This tool is copyright 2010 by Peter Cock, SCRI, UK. All rights reserved. |
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13 See the licence text below. |
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14 |
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15 This tool is a short Python script (using the Galaxy library functions) which |
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16 divides a FASTQ file in two, those sequences with or without an ID present in |
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17 the specified column(s) of a tabular file. Example uses include filtering based |
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18 on search results from a tool like NCBI BLAST before assembly. |
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19 |
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20 There are just two files to install: |
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21 |
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22 * fastq_filter_by_id.py (the Python script) |
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23 * fastq_filter_by_id.xml (the Galaxy tool definition) |
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24 |
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25 The suggested location is next to the similarly named fastq_filter.py and |
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26 fastq_filter.xml files which are included with Galaxy, i.e. in the Galaxy |
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27 folder tools/fastq |
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28 |
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29 You will also need to modify the tools_conf.xml file to tell Galaxy to offer |
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30 the tool. The suggested location is next to the fastq_filter.xml entry. Simply |
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31 add the line: |
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32 |
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33 <tool file="fastq/fastq_filter_by_id.xml" /> |
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34 |
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35 That's it. |
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36 |
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37 |
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38 History |
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39 ======= |
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40 |
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41 v0.0.1 - Initial verion (not publicly released) |
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42 v0.0.2 - Allow both, just pos or just neg output files |
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43 - Preserve the FASTQ variant in the XML wrapper |
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44 v0.0.3 - Fixed bug when generating non-matching FASTQ file only |
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45 v0.0.4 - Deprecated, marked as hidden in the XML |
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46 |
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47 |
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48 Developers |
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49 ========== |
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50 |
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51 This script and related tools are being developed on the following hg branch: |
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52 http://bitbucket.org/peterjc/galaxy-central/src/tools |
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53 |
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54 This incorporates the previously used hg branch: |
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55 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter |
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56 |
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57 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use |
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58 the following command from the Galaxy root folder: |
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59 |
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60 tar -czf fastq_filter_by_id.tar.gz tools/fastq/fastq_filter_by_id.* |
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61 |
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62 Check this worked: |
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63 |
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64 $ tar -tzf fastq_filter_by_id.tar.gz |
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65 fastq/fastq_filter_by_id.py |
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66 fastq/fastq_filter_by_id.txt |
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67 fastq/fastq_filter_by_id.xml |
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68 |
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69 |
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70 Licence (MIT/BSD style) |
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71 ======================= |
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72 |
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73 Permission to use, copy, modify, and distribute this software and its |
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74 documentation with or without modifications and for any purpose and |
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75 without fee is hereby granted, provided that any copyright notices |
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76 appear in all copies and that both those copyright notices and this |
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77 permission notice appear in supporting documentation, and that the |
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78 names of the contributors or copyright holders not be used in |
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79 advertising or publicity pertaining to distribution of the software |
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80 without specific prior permission. |
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81 |
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82 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL |
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83 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED |
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84 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE |
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85 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT |
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86 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS |
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87 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE |
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88 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE |
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89 OR PERFORMANCE OF THIS SOFTWARE. |