Mercurial > repos > peterjc > seq_primer_clip
annotate tools/primers/seq_primer_clip.txt @ 1:06e6112091aa draft
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
| author | peterjc |
|---|---|
| date | Tue, 30 Apr 2013 11:04:13 -0400 |
| parents | b8ca95338e77 |
| children |
| rev | line source |
|---|---|
| 0 | 1 Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads |
| 2 =========================================================== | |
| 3 | |
| 4 This tool is copyright 2011 by Peter Cock, The James Hutton Institute | |
| 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | |
| 6 See the licence text below. | |
| 7 | |
| 8 This tool is a short Python script (using the Galaxy library functions and | |
| 9 Biopython). There are just two files to install: | |
| 10 | |
| 11 * seq_primer_clip.py (the Python script) | |
| 12 * seq_primer_clip.xml (the Galaxy tool definition) | |
| 13 | |
| 14 The suggested location is a new tools/primers folder. You will also need to | |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
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15 modify the tools_conf.xml file to tell Galaxy to offer the tool: |
| 0 | 16 |
| 17 <tool file="primers/seq_primer_clip.xml" /> | |
| 18 | |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
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changeset
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19 If you wish to run the unit tests, also add this to tools_conf.xml.sample |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
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20 and move/copy the test-data files under Galaxy's test-data folder. Then: |
| 0 | 21 |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
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22 $ ./run_functional_tests.sh -id seq_primer_clip |
| 0 | 23 |
| 24 You will also need to install Biopython 1.54 or later. That's it. | |
| 25 | |
| 26 | |
| 27 History | |
| 28 ======= | |
| 29 | |
| 30 v0.0.1 - Initial version (not publicly released) | |
| 31 v0.0.2 - Sort primers by length (longest and therefore most specific first) | |
| 32 v0.0.3 - Consider missing bases at start/end of read as mismatches | |
| 33 v0.0.4 - Apply minimum length to sequences with no match too | |
| 34 v0.0.5 - Count clipped & non-matched short reads separately, length bug fixes | |
| 35 v0.0.6 - Added some functional tests | |
| 36 v0.0.7 - Added error check for bad filename arguments | |
| 37 v0.0.8 - Record version of Python script when run from Galaxy. | |
| 38 - Check for errors using Python script's return code. | |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
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changeset
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39 v0.0.9 - Moved test data to workaround Galaxy Tool Shed limititation. |
| 0 | 40 |
| 41 | |
| 42 Developers | |
| 43 ========== | |
| 44 | |
| 45 This script and related tools are being developed on the following hg branch: | |
| 46 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
| 47 | |
| 48 This incorporates the previously used hg branch: | |
| 49 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter | |
| 50 | |
| 51 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | |
| 52 the following command from the Galaxy root folder: | |
| 53 | |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
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54 $ tar -czf seq_primer_clip.tar.gz tools/primers/seq_primer_clip.* test-data/dop_primers.fasta test-data/MID4_GLZRM4E04_rnd30* |
| 0 | 55 |
| 56 Check this worked: | |
| 57 | |
| 58 $ tar -tzf seq_primer_clip.tar.gz | |
| 59 tools/primers/seq_primer_clip.py | |
| 60 tools/primers/seq_primer_clip.txt | |
| 61 tools/primers/seq_primer_clip.xml | |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
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diff
changeset
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62 test-data/dop_primers.fasta |
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06e6112091aa
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peterjc
parents:
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diff
changeset
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63 test-data/MID4_GLZRM4E04_rnd30.fasta |
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06e6112091aa
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peterjc
parents:
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diff
changeset
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64 test-data/MID4_GLZRM4E04_rnd30.fastqsanger |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
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diff
changeset
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65 test-data/MID4_GLZRM4E04_rnd30_fclip.fasta |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
0
diff
changeset
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66 test-data/MID4_GLZRM4E04_rnd30_fclip.fastqsanger |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
0
diff
changeset
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67 test-data/MID4_GLZRM4E04_rnd30_fclip.sff |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
0
diff
changeset
|
68 test-data/MID4_GLZRM4E04_rnd30_frclip.fasta |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
0
diff
changeset
|
69 test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger |
|
06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
0
diff
changeset
|
70 test-data/MID4_GLZRM4E04_rnd30_frclip.sff |
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06e6112091aa
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
peterjc
parents:
0
diff
changeset
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71 test-data/MID4_GLZRM4E04_rnd30.sff |
| 0 | 72 |
| 73 | |
| 74 Licence (MIT/BSD style) | |
| 75 ======================= | |
| 76 | |
| 77 Permission to use, copy, modify, and distribute this software and its | |
| 78 documentation with or without modifications and for any purpose and | |
| 79 without fee is hereby granted, provided that any copyright notices | |
| 80 appear in all copies and that both those copyright notices and this | |
| 81 permission notice appear in supporting documentation, and that the | |
| 82 names of the contributors or copyright holders not be used in | |
| 83 advertising or publicity pertaining to distribution of the software | |
| 84 without specific prior permission. | |
| 85 | |
| 86 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
| 87 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
| 88 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
| 89 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
| 90 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
| 91 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
| 92 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
| 93 OR PERFORMANCE OF THIS SOFTWARE. |