Mercurial > repos > peterjc > fastq_paired_unpaired
annotate tools/fastq_paired_unpaired/README.rst @ 9:422724644e24 draft
"Update all the pico_galaxy tools on main Tool Shed"
author | peterjc |
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date | Fri, 16 Apr 2021 22:47:43 +0000 |
parents | 8cbc866b72ce |
children | 4851620acfda |
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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 2010-2017 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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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 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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17 |
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18 |
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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 |
5 | 23 the tool from the Galaxy Tool Shed, and Biopython, and allow you to run the unit |
24 tests. | |
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25 |
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26 |
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27 Manual Installation |
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28 =================== |
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29 |
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30 There are just two files to install: |
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31 |
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32 * ``fastq_paired_unpaired.py`` (the Python script) |
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33 * ``fastq_paired_unpaired.xml`` (the Galaxy tool definition) |
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34 |
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35 The suggested location is in the Galaxy folder tools/fastq next to other FASTQ |
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36 tools provided with Galaxy. |
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37 |
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38 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer |
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39 the tool. One suggested location is next to the ``fastq_filter.xml`` entry, or use |
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40 a dedicated folder like ``tools/fastq_paired_unpaired``. Then simply add the line:: |
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41 |
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42 <tool file="fastq_paired_unpaired/fastq_paired_unpaired.xml" /> |
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43 |
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44 That's it. |
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45 |
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46 |
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47 History |
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48 ======= |
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49 |
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50 ======= ====================================================================== |
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51 Version Changes |
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52 ------- ---------------------------------------------------------------------- |
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53 v0.0.1 - Initial version, using Biopython |
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54 v0.0.2 - Help text; cope with multiple pairs per template |
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55 v0.0.3 - Galaxy XML wrappers added |
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56 v0.0.4 - Use Galaxy library to handle FASTQ files (avoid Biopython dependency) |
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57 v0.0.5 - Handle Illumina 1.8 style pair names |
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58 v0.0.6 - Record script version when run from Galaxy |
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59 - Added unit test (FASTQ file using Sanger naming) |
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60 v0.0.7 - Link to Tool Shed added to help text and this documentation. |
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61 v0.0.8 - Use reStructuredText for this README file. |
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62 - Adopt standard MIT License. |
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63 - Updated citation information (Cock et al. 2013). |
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64 - Development moved to GitHub. |
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65 v0.0.9 - Renamed folder and adopted README.rst naming. |
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66 - Removed some unused code in the Python script. |
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67 v0.1.0 - Switch to using Biopython (easier to use script outside of Galaxy). |
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68 - Leaves FASTQ plus lines blank (smaller output files). |
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69 - Tool definition now embeds citation information. |
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70 v0.1.1 - Reorder XML elements (internal change only). |
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71 - Use ``format_source=...`` tag. |
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72 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). |
5 | 73 v0.1.2 - Belatedly declare Biopython dependency via Tool Shed. |
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74 v0.1.3 - Minor internal changes to Python script for error reporting & style. |
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75 - Updated to point at Biopython 1.67 (latest version in Tool Shed). |
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76 - Explicit dependency on ``galaxy_sequence_utils``. |
7 | 77 v0.1.4 - Use ``<command detect_errors="aggressive">`` (internal change only). |
78 - Single quote command line arguments (internal change only). | |
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79 ======= ====================================================================== |
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80 |
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81 |
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82 Developers |
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83 ========== |
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84 |
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85 This script and other tools for filtering FASTA, FASTQ and SFF files were |
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86 initially developed on the following hg branch: |
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87 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter |
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88 |
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89 Development has now moved to a dedicated GitHub repository: |
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90 https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired |
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91 |
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92 For pushing a release to the test or main "Galaxy Tool Shed", use the following |
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93 Planemo commands (which requires you have set your Tool Shed access details in |
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94 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: |
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95 |
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96 $ planemo shed_update -t testtoolshed --check_diff tools/fastq_paired_unpaired/ |
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97 ... |
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98 |
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99 or:: |
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100 |
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101 $ planemo shed_update -t toolshed --check_diff tools/fastq_paired_unpaired/ |
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102 ... |
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103 |
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104 To just build and check the tar ball, use:: |
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105 |
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106 $ planemo shed_upload --tar_only tools/fastq_paired_unpaired/ |
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107 ... |
8 | 108 $ tar -tzf shed_upload.tar.gz |
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109 test-data/sanger-pairs-forward.fastq |
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110 test-data/sanger-pairs-interleaved.fastq |
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111 test-data/sanger-pairs-mixed.fastq |
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112 test-data/sanger-pairs-reverse.fastq |
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113 test-data/sanger-pairs-singles.fastq |
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114 tools/fastq_paired_unpaired/README.rst |
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115 tools/fastq_paired_unpaired/fastq_paired_unpaired.py |
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116 tools/fastq_paired_unpaired/fastq_paired_unpaired.xml |
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117 |
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118 |
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119 Licence (MIT) |
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120 ============= |
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121 |
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122 Permission is hereby granted, free of charge, to any person obtaining a copy |
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123 of this software and associated documentation files (the "Software"), to deal |
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124 in the Software without restriction, including without limitation the rights |
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125 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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126 copies of the Software, and to permit persons to whom the Software is |
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127 furnished to do so, subject to the following conditions: |
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128 |
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129 The above copyright notice and this permission notice shall be included in |
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130 all copies or substantial portions of the Software. |
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131 |
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132 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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133 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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134 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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135 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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136 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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137 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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138 THE SOFTWARE. |