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v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
author peterjc
date Fri, 03 Feb 2017 05:34:18 -0500
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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4 This tool is now obsolete, having been replaced by a more general version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 2010-2017 by Peter Cock, The James Hutton Institute
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13 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
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14 See the licence text below (MIT licence).
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16 This tool is a short Python script (using the Galaxy library functions) which
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17 divides a FASTQ file in two, those sequences with or without an ID present in
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18 the specified column(s) of a tabular file. Example uses include filtering based
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19 on search results from a tool like NCBI BLAST before assembly.
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20
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21 There are just two files to install:
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23 * fastq_filter_by_id.py (the Python script)
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24 * fastq_filter_by_id.xml (the Galaxy tool definition)
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26 The suggested location is next to the similarly named fastq_filter.py and
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27 fastq_filter.xml files which are included with Galaxy, i.e. in the Galaxy
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28 folder tools/fastq
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29
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30 You will also need to modify the tools_conf.xml file to tell Galaxy to offer
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31 the tool. The suggested location is next to the fastq_filter.xml entry. Simply
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32 add the line:
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34 <tool file="fastq/fastq_filter_by_id.xml" />
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36 That's it.
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39 History
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40 =======
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41
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42 ======= ======================================================================
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43 Version Changes
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44 ------- ----------------------------------------------------------------------
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45 v0.0.1 - Initial verion (not publicly released)
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46 v0.0.2 - Allow both, just pos or just neg output files
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47 - Preserve the FASTQ variant in the XML wrapper
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48 v0.0.3 - Fixed bug when generating non-matching FASTQ file only
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49 v0.0.4 - Deprecated, marked as hidden in the XML
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50 v0.0.5 - Explicit dependency on ``galaxy_sequence_utils``.
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51 - Citation information (Cock et al. 2013).
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52 - Explicitly record version via ``<version_command>``.
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53 - Use ``format_source``/``metadata_source`` idiom for output format.
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54 - Use standard MIT license (was previously using the MIT/BSD style
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55 Biopython Licence Agreement).
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56 ======= ======================================================================
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57
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58
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59 Developers
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60 ==========
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61
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62 This script and other tools for filtering FASTA, FASTQ and SFF files were
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63 initially developed on the following hg branches:
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64 http://bitbucket.org/peterjc/galaxy-central/src/tools
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65 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
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66
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67 It is now under GitHub https://github.com/peterjc/pico_galaxy/
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68
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69 For pushing a release to the test or main "Galaxy Tool Shed", use the following
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70 Planemo commands (which requires you have set your Tool Shed access details in
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71 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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72
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73 $ planemo shed_update -t testtoolshed --check_diff tools/fastq_filter_by_id/
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74 ...
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76 or::
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77
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78 $ planemo shed_update -t toolshed --check_diff tools/fastq_filter_by_id/
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79 ...
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80
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81 To just build and check the tar ball, use::
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82
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83 $ planemo shed_upload --tar_only tools/fastq_filter_by_id/
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84 ...
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85 $ tar -tzf shed_upload.tar.gz
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86 tools/fastq_filter_by_id/README.rst
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87 tools/fastq_filter_by_id/fastq_filter_by_id.py
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88 tools/fastq_filter_by_id/fastq_filter_by_id.xml
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89 tools/fastq_filter_by_id/tool_dependencies.xml
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90 test-data/empty_file.dat
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91 test-data/sanger-pairs-mixed.fastq
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92 test-data/sanger-pairs-names.tabular
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93
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94
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95 Licence (MIT)
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96 =============
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97
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98 Permission is hereby granted, free of charge, to any person obtaining a copy
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99 of this software and associated documentation files (the "Software"), to deal
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100 in the Software without restriction, including without limitation the rights
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101 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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102 copies of the Software, and to permit persons to whom the Software is
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103 furnished to do so, subject to the following conditions:
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104
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105 The above copyright notice and this permission notice shall be included in
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106 all copies or substantial portions of the Software.
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107
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108 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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109 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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110 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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111 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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112 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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113 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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114 THE SOFTWARE.