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