Mercurial > repos > peterjc > seq_primer_clip
annotate tools/primers/seq_primer_clip.txt.orig @ 1:8c02a91a8680 draft
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
author | peterjc |
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date | Tue, 30 Apr 2013 11:04:43 -0400 |
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1 Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads |
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2 =========================================================== |
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3 |
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4 This tool is copyright 2011 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. |
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7 |
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8 This tool is a short Python script (using the Galaxy library functions and |
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9 Biopython). There are just two files to install: |
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10 |
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11 * seq_primer_clip.py (the Python script) |
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12 * seq_primer_clip.xml (the Galaxy tool definition) |
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13 |
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14 The suggested location is a new tools/primers folder. You will also need to |
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15 modify the tools_conf.xml file to tell Galaxy to offer the tool and also do |
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16 this to tools_conf.xml.sample in order to run the tests: |
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17 |
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18 <tool file="primers/seq_primer_clip.xml" /> |
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19 |
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20 There are optionally some example files required to run the functional tests, |
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21 put these in the test-data/primers folder. |
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22 |
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23 test-data/primers/dop_primers.fasta |
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24 test-data/primers/MID4_GLZRM4E04_rnd30.fasta |
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25 test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger |
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26 test-data/primers/MID4_GLZRM4E04_rnd30.sff |
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27 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta |
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28 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger |
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29 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff |
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30 |
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31 You should then be able to run the tests with: |
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32 |
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33 sh run_functional_tests.sh -id seq_primer_clip |
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34 |
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35 You will also need to install Biopython 1.54 or later. 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 version (not publicly released) |
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42 v0.0.2 - Sort primers by length (longest and therefore most specific first) |
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43 v0.0.3 - Consider missing bases at start/end of read as mismatches |
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44 v0.0.4 - Apply minimum length to sequences with no match too |
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45 v0.0.5 - Count clipped & non-matched short reads separately, length bug fixes |
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46 v0.0.6 - Added some functional tests |
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47 v0.0.7 - Added error check for bad filename arguments |
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48 v0.0.8 - Record version of Python script when run from Galaxy. |
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49 - Check for errors using Python script's return code. |
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50 |
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51 |
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52 Developers |
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53 ========== |
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54 |
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55 This script and related tools are being developed on the following hg branch: |
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56 http://bitbucket.org/peterjc/galaxy-central/src/tools |
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57 |
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58 This incorporates the previously used hg branch: |
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59 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter |
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60 |
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61 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use |
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62 the following command from the Galaxy root folder: |
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63 |
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64 $ tar -czf seq_primer_clip.tar.gz tools/primers/seq_primer_clip.* test-data/primers/* |
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65 |
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66 Check this worked: |
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67 |
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68 $ tar -tzf seq_primer_clip.tar.gz |
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69 tools/primers/seq_primer_clip.py |
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70 tools/primers/seq_primer_clip.txt |
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71 tools/primers/seq_primer_clip.xml |
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72 test-data/primers/dop_primers.fasta |
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73 test-data/primers/MID4_GLZRM4E04_rnd30.fasta |
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74 test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger |
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75 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta |
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76 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger |
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77 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff |
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78 test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fasta |
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79 test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger |
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80 test-data/primers/MID4_GLZRM4E04_rnd30_frclip.sff |
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81 test-data/primers/MID4_GLZRM4E04_rnd30.sff |
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82 |
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83 |
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84 Licence (MIT/BSD style) |
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85 ======================= |
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86 |
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87 Permission to use, copy, modify, and distribute this software and its |
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88 documentation with or without modifications and for any purpose and |
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89 without fee is hereby granted, provided that any copyright notices |
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90 appear in all copies and that both those copyright notices and this |
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91 permission notice appear in supporting documentation, and that the |
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92 names of the contributors or copyright holders not be used in |
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93 advertising or publicity pertaining to distribution of the software |
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94 without specific prior permission. |
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95 |
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96 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL |
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97 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED |
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98 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE |
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99 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT |
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100 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS |
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101 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE |
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102 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE |
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103 OR PERFORMANCE OF THIS SOFTWARE. |