Mercurial > repos > peterjc > fastq_paired_unpaired
annotate tools/fastq/fastq_paired_unpaired.txt @ 2:95a632a71951 draft
Uploaded v0.0.6, adds unit test
author | peterjc |
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date | Tue, 30 Apr 2013 14:08:37 -0400 |
parents | 7ed81e36fc1c |
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1 Galaxy tool to divide FASTQ files into paired and unpaired reads |
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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 Biopython library functions) which |
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8 divides a FASTQ file into paired reads, and single or orphan reads. You can have |
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9 separate files for the forward/reverse reads, or have them interleaved in a |
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10 single file. |
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11 |
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12 Note that the FASTQ variant is unimportant (Sanger, Solexa, Illumina, or even |
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13 Color Space should all work equally well). |
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14 |
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15 There are just two files to install: |
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16 |
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17 * fastq_paired_unpaired.py (the Python script) |
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18 * fastq_paired_unpaired.xml (the Galaxy tool definition) |
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19 |
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20 The suggested location is in the Galaxy folder tools/fastq next to other FASTQ |
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21 tools provided with Galaxy. |
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22 |
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23 You will also need to modify the tools_conf.xml file to tell Galaxy to offer |
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24 the tool. One suggested location is next to the fastq_filter.xml entry. Simply |
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25 add the line: |
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26 |
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27 <tool file="fastq/fastq_paired_unpaired.xml" /> |
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28 |
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29 That's it. |
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30 |
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31 |
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32 History |
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33 ======= |
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34 |
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35 v0.0.1 - Initial version, using Biopython |
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36 v0.0.2 - Help text; cope with multiple pairs per template |
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37 v0.0.3 - Galaxy XML wrappers added |
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38 v0.0.4 - Use Galaxy library to handle FASTQ files (avoid Biopython dependency) |
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39 v0.0.5 - Handle Illumina 1.8 style pair names |
2 | 40 v0.0.6 - Record script version when run from Galaxy |
41 - Added unit test (FASTQ file using Sanger naming) | |
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42 |
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43 |
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44 Developers |
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45 ========== |
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46 |
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47 This script and other tools for filtering FASTA, FASTQ and SFF files are |
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48 currently being developed on the following hg branch: |
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49 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter |
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50 |
2 | 51 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use |
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52 the following command from the Galaxy root folder: |
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53 |
2 | 54 $ tar -czf fastq_paired_unpaired.tar.gz tools/fastq/fastq_paired_unpaired.* test-data/sanger-pairs-*.fastq |
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55 |
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56 Check this worked: |
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57 |
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58 $ tar -tzf fastq_paired_unpaired.tar.gz |
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59 fastq/fastq_paired_unpaired.py |
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60 fastq/fastq_paired_unpaired.txt |
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61 fastq/fastq_paired_unpaired.xml |
2 | 62 test-data/sanger-pairs-forward.fastq |
63 test-data/sanger-pairs-interleaved.fastq | |
64 test-data/sanger-pairs-mixed.fastq | |
65 test-data/sanger-pairs-reverse.fastq | |
66 test-data/sanger-pairs-singles.fastq | |
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67 |
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68 |
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69 Licence (MIT/BSD style) |
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70 ======================= |
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71 |
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72 Permission to use, copy, modify, and distribute this software and its |
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73 documentation with or without modifications and for any purpose and |
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74 without fee is hereby granted, provided that any copyright notices |
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75 appear in all copies and that both those copyright notices and this |
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76 permission notice appear in supporting documentation, and that the |
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77 names of the contributors or copyright holders not be used in |
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78 advertising or publicity pertaining to distribution of the software |
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79 without specific prior permission. |
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80 |
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81 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL |
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82 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED |
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83 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE |
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84 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT |
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85 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS |
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86 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE |
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87 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE |
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88 OR PERFORMANCE OF THIS SOFTWARE. |