Ross Lazarus
ee6bd2cf46
Changes to allow all test outputs generated by twill to be saved to a folder pointed to by
...
an environment variable "GALAXY_TEST_SAVE" if defined before running functional tests
If the environment variable is empty, all tests procede as usual and test outputs are deleted
without saving
2011-04-14 08:09:48 -04:00
Jeremy Goecks
1a371da9ae
Add tool 'Filter GTF by attribute values list.' Tool filters a GTF based on a list of attribute values; this tool is especially useful as a downstream analysis tool for filtering GTF files based on Cuffdiff outputs. Functional tests are included as well.
2011-04-11 09:39:55 -04:00
Kelly Vincent
72c21e0067
Removed unnecessary size check on BAM file produce in view step of sam-to-bam
2011-04-08 12:06:28 -04:00
Jeremy Goecks
3171c8b024
Fix hyperlinks in Cuffcompare and Cuffdiff documentation.
2011-04-07 16:28:56 -04:00
Kanwei Li
af3f4a2ff9
More BLAST tests
2011-04-06 12:38:00 -04:00
Ross Lazarus
70c8eccee0
change to weblogo test jpg comparison and code cleanups to rgCaCo
2011-04-05 14:07:10 -04:00
Ross Lazarus
a22e453676
merge
2011-04-05 13:57:14 -04:00
Jeremy Goecks
6416659211
Refactor and enhance trackster visual analytics: (a) move all visual analytics code into Tool class for encapsulation; (b) put tool outputs in appropriate history when user is rerunning his own tool; (c) enable users not logged in to run tools; (d) use tool HTML to display inputs rather than sliders.
2011-04-05 11:51:48 -04:00
Kanwei Li
b5d8d577ca
BLAST test changes
2011-04-04 12:55:33 -04:00
Jeremy Goecks
11ec423833
Do not use from_work_dir in Tophat because it causes set_metadata to fail on BAM output when run on a cluster.
2011-04-01 11:36:55 -04:00
Jeremy Goecks
cf3dc6ac01
Trackster: add BED and GFF support to visual analytics framework, and enable GOPS intersect and subtract tools to work with visual analytics.
2011-03-30 11:44:08 -04:00
Ross Lazarus
477b0b9687
minor tweaks to rgCaCo.py
2011-03-27 19:50:50 -04:00
Ross Lazarus
e48fa9d537
Remove bogus makeGFF from rgutils
2011-03-25 13:26:40 -04:00
Ross Lazarus
597a3d006f
Remove bogus makeGFF from rgutils
2011-03-25 13:21:13 -04:00
Ross Lazarus
0c5a868636
Revised rgenetics tools to remove post job hooks
2011-03-25 13:12:21 -04:00
Jeremy Goecks
f138afb629
Add selected attribute to default value for Tophat coverage search.
2011-03-24 20:29:40 -04:00
Jeremy Goecks
4e4ca2d542
Change default value for Tophat coverage search to true.
2011-03-24 17:36:06 -04:00
Richard Burhans
f67ab3c70c
fixed calculation of codon starts
2011-03-24 15:03:12 -04:00
Daniel Blankenberg
8bdda93ffc
Add more verbose error reporting to FASTQ Groomer tool.
2011-03-24 11:45:50 -04:00
Ross Lazarus
dc4b62c740
still having a problem with getting clustalw2 to print sequence indices - test does not cover so passes
2011-03-23 19:32:32 -04:00
Ross Lazarus
579cefd5f9
python wrapper for clustalw tool
2011-03-23 19:14:14 -04:00
Ross Lazarus
76b86b9762
Fixes to clustalw tool - need a python wrapper to take care of Clustalw's bad habit of writing to an output path determined from the input path - naughty..Also added the dendrogram to the log output so test output sample updated; version bumped
2011-03-23 17:18:29 -04:00
Daniel Blankenberg
6d4f4ac309
Remove 'data.file_name = data.file_name' from Rgenetics code files.
2011-03-23 12:41:39 -04:00
Greg Von Kuster
8ba7de4c8b
Improved checking to determine if a bam file is sorted. If the version of samtools being used is 0.1.13 or newer, determination of bam sorting is now much more robust. Add a new functional test to the test_library_features script that tests uploading a library_dataset (where the file is an unsorted bam file) using a combination of 'upload_paths' and 'link_to_files'. Rename the test-data file previously named 3.bam to now be named 3unsorted.bam to clarify that it is an unsorted bam file.
2011-03-23 12:18:57 -04:00
Ross Lazarus
43ed5f1953
fixed typo that broke weblogo test
2011-03-23 11:46:10 -04:00
Ross Lazarus
3a908497d5
Added subsequence and colour options to weblogo3 sequence logo generator; tweaks to clustalw tool help
2011-03-23 11:20:23 -04:00
Nate Coraor
1fdfacc977
Set the ftype of SRMA test outputs so the BAMs are compared as SAMs
2011-03-23 10:59:26 -04:00
Daniel Blankenberg
58963cc97d
Remove link target from intermine datasource tools.
2011-03-22 20:29:32 -04:00
Kanwei Li
82dde6e37e
Refactor Grouping tool and fix bug where data after a blank value in the group_by column returns the wrong data.
2011-03-22 17:49:09 -04:00
Ross Lazarus
6646cfa80d
Adding two new tool wrappers and tests - clustalw ( http://www.clustal.org ) for multiple alignments and a sequence motif generator based on weblogo3 ( http://weblogo.berkeley.edu ) which works on fasta files such as alignments from clustalw
2011-03-22 14:08:32 -04:00
Richard Burhans
93911caa4f
fixed comment bug and added additional error messages for SIFT tool
2011-03-22 13:45:31 -04:00
Jeremy Goecks
6e61176835
Merge.
2011-03-21 15:24:05 -04:00
Kanwei Li
bfa19d9f64
Typos in tool confs
2011-03-21 13:48:28 -04:00
Jeremy Goecks
f6a601f517
Add count GFF features tool and tests. Tool counts the number of features in a GFF file; this is different than the number of lines b/c GFF features are often multiline.
2011-03-21 13:01:24 -04:00
Daniel Blankenberg
a01df218d7
Update CCAT to version 3.0.
2011-03-16 10:41:38 -04:00
Greg Von Kuster
7640af8e06
Don't alter the contents of a file while uploading to a data library if using the filesystem_paths option. This partially resolves the issue where a supposedly sorted BAM file was being resorted upon upload to a data library when using this option. A better imlementation of determining whether a BAM file has been sorted (so that it does not get resorted) remains to be done.
2011-03-15 09:38:29 -04:00
Greg Von Kuster
df6f94b1d0
Per request from Peter Cock, turn the "Copy data into Galaxy?" check box into a select list that clarifies the behavior. The default is to copy files into Galaxy.
2011-03-11 14:56:11 -05:00
Jeremy Goecks
82ef98f15c
Fix bugs in GFFReaderWrapper so that GFF3 files are read properly. Add GFF3 test to gff_filter_by_feature_count.
2011-03-09 14:22:10 -05:00
Jeremy Goecks
86b7194bff
Use GFFReaderWrapper in gff_filter_by_feature_count tool in order to leverage support for GTF, GFF, and GFF3 found in reader wrapper. This also simplifies the tool considerably.
2011-03-08 19:01:59 -05:00
Kelly Vincent
a4f910c730
Update SRMA test files so that functional tests pass
2011-03-08 16:17:09 -05:00
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
Ross Lazarus