Mercurial > repos > peterjc > seq_primer_clip
comparison tools/primers/seq_primer_clip.txt @ 1:8c02a91a8680 draft
Uploaded v0.0.9, modifies tests to cope with current Tool Shed limitation.
author | peterjc |
---|---|
date | Tue, 30 Apr 2013 11:04:43 -0400 |
parents | 945053d79e60 |
children |
comparison
equal
deleted
inserted
replaced
0:945053d79e60 | 1:8c02a91a8680 |
---|---|
10 | 10 |
11 * seq_primer_clip.py (the Python script) | 11 * seq_primer_clip.py (the Python script) |
12 * seq_primer_clip.xml (the Galaxy tool definition) | 12 * seq_primer_clip.xml (the Galaxy tool definition) |
13 | 13 |
14 The suggested location is a new tools/primers folder. You will also need to | 14 The suggested location is a new tools/primers folder. You will also need to |
15 modify the tools_conf.xml file to tell Galaxy to offer the tool and also do | 15 modify the tools_conf.xml file to tell Galaxy to offer the tool: |
16 this to tools_conf.xml.sample in order to run the tests: | |
17 | 16 |
18 <tool file="primers/seq_primer_clip.xml" /> | 17 <tool file="primers/seq_primer_clip.xml" /> |
19 | 18 |
20 There are optionally some example files required to run the functional tests, | 19 If you wish to run the unit tests, also add this to tools_conf.xml.sample |
21 put these in the test-data/primers folder. | 20 and move/copy the test-data files under Galaxy's test-data folder. Then: |
22 | 21 |
23 test-data/primers/dop_primers.fasta | 22 $ ./run_functional_tests.sh -id seq_primer_clip |
24 test-data/primers/MID4_GLZRM4E04_rnd30.fasta | |
25 test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger | |
26 test-data/primers/MID4_GLZRM4E04_rnd30.sff | |
27 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta | |
28 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger | |
29 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff | |
30 | |
31 You should then be able to run the tests with: | |
32 | |
33 sh run_functional_tests.sh -id seq_primer_clip | |
34 | 23 |
35 You will also need to install Biopython 1.54 or later. That's it. | 24 You will also need to install Biopython 1.54 or later. That's it. |
36 | 25 |
37 | 26 |
38 History | 27 History |
45 v0.0.5 - Count clipped & non-matched short reads separately, length bug fixes | 34 v0.0.5 - Count clipped & non-matched short reads separately, length bug fixes |
46 v0.0.6 - Added some functional tests | 35 v0.0.6 - Added some functional tests |
47 v0.0.7 - Added error check for bad filename arguments | 36 v0.0.7 - Added error check for bad filename arguments |
48 v0.0.8 - Record version of Python script when run from Galaxy. | 37 v0.0.8 - Record version of Python script when run from Galaxy. |
49 - Check for errors using Python script's return code. | 38 - Check for errors using Python script's return code. |
39 v0.0.9 - Moved test data to workaround Galaxy Tool Shed limititation. | |
50 | 40 |
51 | 41 |
52 Developers | 42 Developers |
53 ========== | 43 ========== |
54 | 44 |
59 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter | 49 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter |
60 | 50 |
61 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | 51 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use |
62 the following command from the Galaxy root folder: | 52 the following command from the Galaxy root folder: |
63 | 53 |
64 $ tar -czf seq_primer_clip.tar.gz tools/primers/seq_primer_clip.* test-data/primers/* | 54 $ tar -czf seq_primer_clip.tar.gz tools/primers/seq_primer_clip.* test-data/dop_primers.fasta test-data/MID4_GLZRM4E04_rnd30* |
65 | 55 |
66 Check this worked: | 56 Check this worked: |
67 | 57 |
68 $ tar -tzf seq_primer_clip.tar.gz | 58 $ tar -tzf seq_primer_clip.tar.gz |
69 tools/primers/seq_primer_clip.py | 59 tools/primers/seq_primer_clip.py |
70 tools/primers/seq_primer_clip.txt | 60 tools/primers/seq_primer_clip.txt |
71 tools/primers/seq_primer_clip.xml | 61 tools/primers/seq_primer_clip.xml |
72 test-data/primers/dop_primers.fasta | 62 test-data/dop_primers.fasta |
73 test-data/primers/MID4_GLZRM4E04_rnd30.fasta | 63 test-data/MID4_GLZRM4E04_rnd30.fasta |
74 test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger | 64 test-data/MID4_GLZRM4E04_rnd30.fastqsanger |
75 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta | 65 test-data/MID4_GLZRM4E04_rnd30_fclip.fasta |
76 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger | 66 test-data/MID4_GLZRM4E04_rnd30_fclip.fastqsanger |
77 test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff | 67 test-data/MID4_GLZRM4E04_rnd30_fclip.sff |
78 test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fasta | 68 test-data/MID4_GLZRM4E04_rnd30_frclip.fasta |
79 test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger | 69 test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger |
80 test-data/primers/MID4_GLZRM4E04_rnd30_frclip.sff | 70 test-data/MID4_GLZRM4E04_rnd30_frclip.sff |
81 test-data/primers/MID4_GLZRM4E04_rnd30.sff | 71 test-data/MID4_GLZRM4E04_rnd30.sff |
82 | 72 |
83 | 73 |
84 Licence (MIT/BSD style) | 74 Licence (MIT/BSD style) |
85 ======================= | 75 ======================= |
86 | 76 |