 Nate Coraor
|
a221548e8f
|
An uninitialized value in R's PDF driver was causing it to sometimes randomly add a few elements to PDF outputs. The bug has been fixed in the buildbot environment and these changes account for that fix.
|
2011-03-08 11:17:57 -05:00 |
|
|
Jeremy Goecks
|
0030c2c810
|
Fix bug in output for gff_filter_by_feature_count tool.
|
2011-03-07 15:53:31 -05:00 |
|
|
Guruprasad Anada
|
4a81da484c
|
Updated tool help for microsatellite birth/death tools.
|
2011-03-07 13:30:37 -05:00 |
|
|
Nate Coraor
|
e3f970a36f
|
Use lines_diff on the pdf outputs of various R-based tools.
|
2011-03-03 12:21:44 -05:00 |
|
|
Daniel Blankenberg
|
4685ec3f8a
|
Enhance Bowtie wrapper to accept non-sanger variant FASTQ files.
|
2011-03-02 11:40:58 -05:00 |
|
|
Ramkrishna Chakrabarty
|
bdb4ec4505
|
Fix for vcf_extract tool test
|
2011-03-02 09:40:10 -05:00 |
|
|
Dannon Baker
|
a9548d1a07
|
Remove ftype from mosaik/freebayes test outputs.
|
2011-03-02 08:38:19 -05:00 |
|
|
Nate Coraor
|
0411837b7b
|
Drop the ftype attribute from tophat test outputs
|
2011-03-02 08:28:30 -05:00 |
|
|
Nate Coraor
|
3fc4c7c4f8
|
Enable the ftype attribute for test outputs, fixes the sam-to-bam test.
|
2011-03-01 15:46:35 -05:00 |
|
|
Nate Coraor
|
cb9bbd0e0b
|
Update bwa_color_wrapper cached indices name to match the key used in the test data repository
|
2011-03-01 15:21:25 -05:00 |
|
|
Daniel Blankenberg
|
5bff82eb46
|
Have YeastMine datasource tool point to the production server location and add configuration to tool_conf.xml.main.
|
2011-03-01 13:00:27 -05:00 |
|
|
Daniel Blankenberg
|
7fb03e7768
|
Remove unused parameters from TopHat and Cufflinks tool tests.
|
2011-02-28 15:17:35 -05:00 |
|
|
Ramkrishna Chakrabarty
|
58284e4848
|
Adding tests for vcf extract and filter tools
|
2011-02-28 15:03:45 -05:00 |
|
|
Dannon Baker
|
48b65e9b17
|
mosaik: Test case uses sim_size instead of diff now, to get around the changing RG tag.
|
2011-02-28 14:32:36 -05:00 |
|
|
Guruprasad Anada
|
4a94876feb
|
Fixed functional test for 'compute q values' tool - q-value is rounded to 6 significant digits, which shouldn't differ between different runs of the tool.
Also, fixed a bug in microsatellite birth/death tool - cases where microsatellite boundaries aren't defined are skipped.
|
2011-02-28 14:04:53 -05:00 |
|
|
Daniel Blankenberg
|
4eb1b0a79f
|
Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.
|
2011-02-28 12:16:28 -05:00 |
|
|
Jeremy Goecks
|
09cd28148f
|
Fix bad value in cufflinks functional test.
|
2011-02-28 09:59:30 -05:00 |
|
|
Jeremy Goecks
|
c5ac00b7db
|
Suppress most logging for cufflinks and cuffdiff as the logging can generate output that is incompatible with UTF-8 format used by database.
|
2011-02-27 14:48:23 -05:00 |
|
|
Dannon Baker
|
4d499816e3
|
Basic Freebayes test added.
|
2011-02-26 10:53:50 -05:00 |
|
|
Dannon Baker
|
11f15b123b
|
Freebayes and Mosaik updates
|
2011-02-25 17:53:58 -05:00 |
|
|
Ramkrishna Chakrabarty
|
974efda97a
|
First pass of extract & filter VCF tools.
|
2011-02-25 15:58:13 -05:00 |
|
|
Kanwei Li
|
43db543f1f
|
Update test-data files for meme 4.6.0
|
2011-02-25 14:58:35 -05:00 |
|
|
Kanwei Li
|
096e95ff41
|
Typos
|
2011-02-25 13:35:27 -05:00 |
|
|
Jeremy Goecks
|
39bfd3c89d
|
Add options to Tophat wrapper to support v1.2.0 functionality: (a) allow indel search; (b) max insertion and max deletion lengths; and (c) library type. Update functional tests to tests new options. Also update function that checks from_work_dir output attribute to use real path to prevent mishandling of symbolic links.
|
2011-02-24 15:24:52 -05:00 |
|
|
Kanwei Li
|
036082793b
|
Fix bed_to_bigBed test
|
2011-02-24 15:23:21 -05:00 |
|
|
Kanwei Li
|
8d203efef1
|
Fix BLAST+ test
|
2011-02-24 15:07:46 -05:00 |
|
|
Kanwei Li
|
dfed222fcb
|
Fix debugging output on BLASTX+ failure
|
2011-02-24 12:27:37 -05:00 |
|
|
Ramkrishna Chakrabarty
|
47a61afa18
|
Adding ftype attribute to vcf tool tests
|
2011-02-24 12:16:33 -05:00 |
|
|
Dannon Baker
|
668d03ba7d
|
Initial commit of Mosaik and Freebayes.
|
2011-02-23 14:01:58 -05:00 |
|
|
Nate Coraor
|
7ef6723533
|
Update bwa_wrapper to use the test data repository. bwa_color_wrapper will need to be done once the test data repository is updated to contain the data it uses.
|
2011-02-23 13:54:06 -05:00 |
|
|
Jeremy Goecks
|
ef28a2cb36
|
Set output dataset type for 'Extract GFF features' tool to be input dataset type.
|
2011-02-22 18:41:15 -05:00 |
|
|
Ramkrishna Chakrabarty
|
b48d817329
|
Adding VCF annotate and intersect tools
|
2011-02-22 15:31:57 -05:00 |
|
|
Guruprasad Anada
|
ff7e8fe2e0
|
Fixed functional tests for the following tools: histogram, estimate indel rates, compute q-values, kernel pca.
|
2011-02-22 12:37:06 -05:00 |
|
|
Nate Coraor
|
f501a13c53
|
Update bowtie_wrapper and bowtie_color_wrapper to use test data from the external test data repository
|
2011-02-21 16:25:35 -05:00 |
|
|
Daniel Blankenberg
|
bde479e1f1
|
Do not print summary information in FASTQ groomer when grooming an empty file.
|
2011-02-18 12:07:27 -05:00 |
|
|
Daniel Blankenberg
|
103b05557e
|
Fix typo in Intersect tool description.
|
2011-02-18 10:42:13 -05:00 |
|
|
Kelly Vincent
|
28ee833a06
|
merge
|
2011-02-17 14:48:53 -05:00 |
|
|
Jeremy Goecks
|
6cc9dd1159
|
Set default value for Cuffdiff's minimum alignment count parameter to reflect v0.9.3
|
2011-02-17 14:25:56 -05:00 |
|
|
Kelly Vincent
|
c0726bfb23
|
Fixed BFAST functional tests (corrected problem with chromosome names in test files)
|
2011-02-17 13:46:40 -05:00 |
|
|
Jeremy Goecks
|
108e3f8494
|
Fix bug in extract_genomic_dna to handle non-GFF files when interpret features is true. Tweak functional test to cover new behavior.
|
2011-02-16 21:46:23 -05:00 |
|
|
Jeremy Goecks
|
ae6cb82e01
|
Bug fix: do not fix strand in extract_genomic_dna tool.
|
2011-02-16 12:56:18 -05:00 |
|
|
Daniel Blankenberg
|
882b98531c
|
Add a Line/Word/Character count Text Manipulation tool.
|
2011-02-15 17:24:24 -05:00 |
|
|
Jeremy Goecks
|
a9d7983ffe
|
Fix attribute bug in cuffcompare wrapper.
|
2011-02-14 17:25:09 -05:00 |
|
|
Jeremy Goecks
|
98a3a358e0
|
Fix bug in extract_genomic_dna.py so that comment lines are correctly handled.
|
2011-02-14 13:21:04 -05:00 |
|
|
Guruprasad Anada
|
02ee54b502
|
Updated path to sputnik binary in 'Extract orthologous microsatellites for multiple (>2) species alignments' tool
|
2011-02-11 09:27:10 -05:00 |
|
|
Jeremy Goecks
|
23a8b191a7
|
Extend extract_genomic_dna tool to support GFF/GTF features and custom genomes. For GFF/GTF files, tool provides option to return sequence data for each feature's intervals, which are split across lines in GFF/GTF files. Tool also now accepts sequence data from a history item, enabling the extraction of data from custom genomes. New functional tests added to cover new functionality.
|
2011-02-10 17:19:40 -05:00 |
|
|
Guruprasad Anada
|
924ea2443b
|
Better handling of complex interrupted microsatellites in 'Extract orthologous microsatellites for multiple species alignments' tool.
|
2011-02-10 10:33:08 -05:00 |
|
|
Daniel Blankenberg
|
8cd2a39cc7
|
Add metabolicMine datasource tool.
|
2011-02-09 15:42:42 -05:00 |
|
|
Nate Coraor
|
409f149aa4
|
Fix for the histogram tool for the "'x' must be numeric" error experienced by some local installations. Thanks, Jim Johnson.
|
2011-02-03 15:52:44 -05:00 |
|
|
Peter Cock
|
2cde9bed73
|
Avoid using shell=True when we call subprocess to ensure if the Python script is killed, so too is the BLAST process
|
2011-02-01 15:24:45 +00:00 |
|