Greg Von Kuster
a8cd7a9118
Streamline the process of adding datasets to a library and then updating roles and permissions on them, improve admin GUI flow, more functional tests.
2008-11-18 17:10:16 -05:00
Greg Von Kuster
5331dee076
Add functioal test baseline support for the repeat construct, more work needed ( e.g., multiple repeat elements, refresh_on_change when the input to be refreshed is within a repeat construct ). Added functional tests for some tools that use this construct.
2008-11-10 14:22:01 -05:00
Wen-Yu Chung
0021c40c85
add shrimp_color_space mapping tool with functional test data.
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add a new datatype called csfasta.
2008-10-13 15:06:42 -04:00
Anton Nekrutenko
f8915c416f
Forgot two test datasets
2008-09-14 14:58:50 -04:00
Guruprasad Anada
4c520e8ce2
Rewrote "convert delimiters to tab" tool in python.
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Modified "Concatenate queries tail-to-head" tool to include multiple queries.
2008-07-02 19:43:08 +00:00
Greg Von Kuster
666de20b4d
Cleanup for fastqsolexa data type converters. We are currently supporting only the Solexa variant and will add support for other variants when the formats stabilize.
2008-06-09 20:15:04 +00:00
Greg Von Kuster
1a23f9e55d
Requires config modification - Add Fastq sniffer, add support for fastqsolexa data type, rename convert_fatsq2fasta tool to be fastq_to_fasta_qual, add functional tests for both fastq and fastqsolexa data types, misc code cleanup.
2008-05-29 19:12:36 +00:00
Greg Von Kuster
57fe2ba4b0
Cleaned up lav_to_bed a bit, added functional test. Removed old, unused tools from the ~/tools/filter directory.
2008-05-28 19:26:42 +00:00
Greg Von Kuster
f7806342fc
Requires change to Galaxy config - fixed the way the File Format select list in the upload tool is dynamically generated, now retrieved from the upload_file_formats in app.registry.
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Fixed all references to 'qualityscore' file extensions to be 'qual', since that is the extension in the QualityScore class.
Added functional test to the fastq2fasta converter.
2008-05-28 16:01:29 +00:00
Wen-Yu Chung
50e24553ae
generate png file instead of pdf file in short read distribution tool.
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add a fastq converting tool.
2008-05-27 18:51:34 +00:00
Wen-Yu Chung
bf61fee03f
update functional test for short read tools that generate pdf output.
2008-04-04 14:59:45 +00:00
Greg Von Kuster
1580ed8260
Functional tests will now properly handle output datasets in pdf format. Added functional tests for histogram and scatterplot. Fixed a bug where temporary files was not removed if functional test failed.
2008-04-04 14:45:29 +00:00
Wen-Yu Chung
9adee0844d
update short reads tools. add functional test data.
2008-03-27 22:11:18 +00:00
Wen-Yu Chung
78802fa73b
add scripts for preparing nt and wgs databases.
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update blastdb location file, wgs is available now.
2008-03-27 17:41:40 +00:00
Wen-Yu Chung
5ba3755ad6
add functional test data for megablast xml parser.
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the functional test is failed due to unknown reasons.
2008-03-25 22:09:54 +00:00
Anton Nekrutenko
a262ac1754
Finalizing taxonomy. Removed taxonomy processing from scripts. This does not require sqlite anymore. Script for fetching taxonomy now uses flat files directly and is much faster
2008-03-20 19:38:31 +00:00
Anton Nekrutenko
d25b346130
Changes to taxonomy fetches and two new datatypes: taxonomy and newick
2008-03-04 20:30:26 +00:00
Anton Nekrutenko
9dca050a79
Fisrt pass on taxonomic rank fetcher
2008-03-03 19:40:36 +00:00
Greg Von Kuster
71f25a7bfa
Fixes for bed_to_gff_converter.
2008-01-28 15:27:33 +00:00
Daniel Blankenberg
02a078da82
Decrease size of gops cluster test data.
2008-01-16 20:21:07 +00:00
Wen-Yu Chung
9f0f822deb
add a section: metagenomics
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tools for running phred(need to change path later), trim sequence, generate boxplot and an array of length of the reads.
test data are added.
trim sequence and array of length passed functional test.
phred (2 ouput files) and boxplot (pdf file) didn't pass functional test yet.
2008-01-09 20:41:59 +00:00
Greg Von Kuster
8b0fe490b1
Reverting the test data for the gops_cluster tool to that which was originally used by Ian in rev 1636.
2008-01-07 13:02:10 +00:00
Greg Von Kuster
59416716eb
Deleted a huge emboss test data file that is not needed. Added binary, zipped and gzipped test data files.
2007-12-20 17:43:05 +00:00
Chinmay Rao
1843e0034c
Adding EMBOSS v5.0 newcpgreport noreturn patmatdb pepinfo pepnet pepwheel pepwindow pepwindowall plotcon pepcoil pepstats plotorf polydot noreturn octanol oddcomp
2007-12-17 14:26:48 +00:00
Chinmay Rao
3539fb038d
Version 5.0 of EMBOSS Antigenic tool.
2007-12-11 15:59:01 +00:00
Greg Von Kuster
71d16671bc
First pass at final phase of cleaning up approach to dynamic select lists. Added a functional test to phastOdds tool. The following tools now use this latest approach to dynamic optioons:
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axt_to_fasta, phastOdds, axt_to_lav, random_intervals, extractAxt_wrapper, axt_to_concat_fasta, aggregate_binned_scores.
2007-11-16 20:08:31 +00:00
Greg Von Kuster
b7190a44c0
2007-10-26 19:28:36 +00:00
Greg Von Kuster
ec1f6a468f
Fixed Bed.sniff() and changed all old bed / interval test data files to work correctly with the new version. Corrected bugs in Gff.set_meta() and Gff3.set_meta(). Commented out test1 in subtract_query.xml until I can determine how to correct twill to properly handle the test with the new approach to using dynamic_options.
2007-10-25 17:18:46 +00:00
Greg Von Kuster
10152d8b27
Eliminating more unused test data.
2007-10-05 19:47:23 +00:00
Greg Von Kuster
dce3f2eed5
Some test data I missed.
2007-10-05 19:10:24 +00:00
Greg Von Kuster
43afaf3969
Added functional tests for sniffing and metadata settings on file upload. Fixed a test in the 'Filter Maf Blocks by size' tool. Added new test data. Commited the bug fix I really wanted in Axt.sniff().
2007-10-05 18:02:33 +00:00
Greg Von Kuster
aa0dcc81d5
More functional test cleanup, eliminated redundant tests, unused test data, and renamed some test data files.
2007-10-04 14:14:15 +00:00
Greg Von Kuster
b3aa4efa6f
Cleaned up functional tests, eliminating some redundant tests and unused test data files. Next step, add many missing tests.
2007-10-03 14:17:41 +00:00
Jianbin He
bd0a5132f3
data change for testing
2007-09-27 19:53:04 +00:00
Greg Von Kuster
6d72d59f09
Fixes for the grouping tool.
2007-08-17 14:23:42 +00:00
Jianbin He
4dbd6b603d
update test data, cf_maf2fasta.dat
2007-06-04 16:12:01 +00:00
Jianbin He
19f1bd4ace
change test data to smaller ones
2007-06-02 03:06:00 +00:00
Jianbin He
ba95acc6a4
remove useless data
2007-06-01 20:53:43 +00:00
Jianbin He
38128dd7aa
change test data to smaller ones
2007-06-01 20:15:01 +00:00
Greg Von Kuster
39f811eff7
Added new Subtract Whole Query tool. Also some miscellaneous code clean-up.
2007-05-07 18:59:15 +00:00
Jianbin He
182d5bd027
update data for nj_tree_newrick aggregate test
2007-04-18 19:54:12 +00:00
Jianbin He
e2f1cc1abb
remove useless data
2007-03-28 14:03:57 +00:00
Jianbin He
091d6fc023
remove load_test
2007-03-27 16:12:27 +00:00
Jianbin He
be2b8d74aa
add data for sc_3E test
2007-03-23 19:30:30 +00:00
Jianbin He
c6dcb4e7dd
change/add some data for testing
2007-03-23 15:30:07 +00:00
David C. King
f3eab4c4ca
cleaned up tests and old script for aggregate(binned) scores
2007-03-13 21:20:31 +00:00
Jianbin He
602290ed90
data for ggs_aggregate_datapoints test
2007-03-13 19:24:15 +00:00
Jianbin He
8c298c47b0
change data for test ggs_aggregate_datapoints and sta_summary; add data for kaks calculator.
2007-03-13 15:55:08 +00:00
Jianbin He
7f1146b3c1
2007-03-12 15:59:13 +00:00
Yi Zhang
6d798fdfef
test data for the test scripts: test_3D_Edit_Modify.py and test_3E_Filter.py
2007-01-18 22:30:27 +00:00
Greg Von Kuster