annotate tools/fastq/fastq_paired_unpaired.rst @ 3:528ba9c896e0 draft

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author peterjc
date Wed, 18 Sep 2013 06:13:27 -0400
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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 2010-2013 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 (MIT licence).
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7
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8 This tool is a short Python script which divides a FASTQ file into paired
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9 reads, and single or orphan reads. You can have separate files for the
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10 forward/reverse reads, or have them interleaved in a single file.
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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 This tool is available from the Galaxy Tool Shed at:
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16 http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired
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19 Automated Installation
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20 ======================
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21
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22 This should be straightforward, Galaxy should automatically download and install
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23 the tool from the Galaxy Tool Shed, and run the unit tests
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26 Manual Installation
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27 ===================
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28
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29 There are just two files to install:
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30
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31 * fastq_paired_unpaired.py (the Python script)
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32 * fastq_paired_unpaired.xml (the Galaxy tool definition)
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34 The suggested location is in the Galaxy folder tools/fastq next to other FASTQ
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35 tools provided with Galaxy.
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36
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37 You will also need to modify the tools_conf.xml file to tell Galaxy to offer
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38 the tool. One suggested location is next to the fastq_filter.xml entry. Simply
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39 add the line::
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41 <tool file="fastq/fastq_paired_unpaired.xml" />
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42
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43 That's it.
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46 History
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47 =======
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49 ======= ======================================================================
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50 Version Changes
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51 ------- ----------------------------------------------------------------------
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52 v0.0.1 - Initial version, using Biopython
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53 v0.0.2 - Help text; cope with multiple pairs per template
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54 v0.0.3 - Galaxy XML wrappers added
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55 v0.0.4 - Use Galaxy library to handle FASTQ files (avoid Biopython dependency)
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56 v0.0.5 - Handle Illumina 1.8 style pair names
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57 v0.0.6 - Record script version when run from Galaxy
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58 - Added unit test (FASTQ file using Sanger naming)
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59 v0.0.7 - Link to Tool Shed added to help text and this documentation.
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60 v0.0.8 - Use reStructuredText for this README file.
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61 - Adopt standard MIT License.
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62 - Updated citation information (Cock et al. 2013).
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63 ======= ======================================================================
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66 Developers
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67 ==========
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68
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69 This script and other tools for filtering FASTA, FASTQ and SFF files were
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70 initially developed on the following hg branch:
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71 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
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72
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73 Development has now moved to a dedicated GitHub repository:
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74 https://github.com/peterjc/pico_galaxy/tree/master/tools/
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75
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76 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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77 the following command from the Galaxy root folder::
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78
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79 $ tar -czf fastq_paired_unpaired.tar.gz tools/fastq/fastq_paired_unpaired.* test-data/sanger-pairs-*.fastq
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80
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81 Check this worked::
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82
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83 $ tar -tzf fastq_paired_unpaired.tar.gz
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84 tools/fastq/fastq_paired_unpaired.py
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85 tools/fastq/fastq_paired_unpaired.rst
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86 tools/fastq/fastq_paired_unpaired.xml
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87 test-data/sanger-pairs-forward.fastq
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88 test-data/sanger-pairs-interleaved.fastq
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89 test-data/sanger-pairs-mixed.fastq
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90 test-data/sanger-pairs-reverse.fastq
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91 test-data/sanger-pairs-singles.fastq
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92
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93
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94 Licence (MIT)
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95 =============
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96
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97 Permission is hereby granted, free of charge, to any person obtaining a copy
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98 of this software and associated documentation files (the "Software"), to deal
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99 in the Software without restriction, including without limitation the rights
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100 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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101 copies of the Software, and to permit persons to whom the Software is
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102 furnished to do so, subject to the following conditions:
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103
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104 The above copyright notice and this permission notice shall be included in
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105 all copies or substantial portions of the Software.
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106
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107 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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108 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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109 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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110 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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111 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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112 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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113 THE SOFTWARE.