galaxy

library

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

users

Fixes and functional tests for uploading directories of files from both the Admin view and the Libraries view ( requires new config setting ).

2009-06-16 09:55:15 -04:00

1.axt

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

1.bed

change test data to smaller ones

2007-06-01 20:15:01 +00:00

1.customtrack

Some test data I missed.

2007-10-05 19:10:24 +00:00

1.fasta

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

1.fastqsanger

Added fastqsanger data format and required bwa_wrapper to take only that format as input

2009-07-30 12:06:24 -04:00

1.fastqsolexa

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

1.interval

Some test data I missed.

2007-10-05 19:10:24 +00:00

1.lav

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

1.sam

Added two new datatypes (sam and bam) and an associated test

2009-08-19 09:13:21 -04:00

1.scf

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

1.tabular

Fixes for the grouping tool.

2007-08-17 14:23:42 +00:00

1.txt

Added new Subtract Whole Query tool. Also some miscellaneous code clean-up.

2007-05-07 18:59:15 +00:00

1.wig

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

2.bed

change test data to smaller ones

2007-06-01 20:15:01 +00:00

2.fasta

Version 5.0 of EMBOSS Antigenic tool.

2007-12-11 15:59:01 +00:00

2.fastqsanger

Added fastqsanger data format and required bwa_wrapper to take only that format as input

2009-07-30 12:06:24 -04:00

2.fastqsolexa

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

2.tabular

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

3.bed

change test data to smaller ones

2007-06-02 03:06:00 +00:00

3.maf

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

4.bed

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:

2007-11-16 20:08:31 +00:00

4.bed.gz

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

5.bed

Decrease size of gops cluster test data.

2008-01-16 20:21:07 +00:00

5.gff

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

5.gff3

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

6.bed

update data for nj_tree_newrick aggregate test

2007-04-18 19:54:12 +00:00

7.bed

change test data to smaller ones

2007-06-02 03:06:00 +00:00

8.bed

2007-10-26 19:28:36 +00:00

8.tabular

More functional test cleanup, eliminated redundant tests, unused test data, and renamed some test data files.

2007-10-04 14:14:15 +00:00

9.bed

Fixes for bed_to_gff_converter.

2008-01-28 15:27:33 +00:00

454Score.pdf

update functional test for short read tools that generate pdf output.

2008-04-04 14:59:45 +00:00

454Score.png

fix for short read score distribution tool. restore test data.

2008-12-19 14:25:43 -05:00

a.tab

Rewrote "convert delimiters to tab" tool in python.

2008-07-02 19:43:08 +00:00

a.txt

Rewrote "convert delimiters to tab" tool in python.

2008-07-02 19:43:08 +00:00

aggregate_binned_scores_in_intervals.bed

cleaned up tests and old script for aggregate(binned) scores

2007-03-13 21:20:31 +00:00

cat_wrapper_out1.bed

restoring original files

2009-02-10 11:54:53 -05:00

emboss_noreturn_out.noreturn

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

eq-condense.dat

change test data to smaller ones

2007-06-01 20:15:01 +00:00

eq-convert.dat

change test data to smaller ones

2007-06-01 20:15:01 +00:00

filter1_test1.bed

More functional test cleanup, eliminated redundant tests, unused test data, and renamed some test data files.

2007-10-04 14:14:15 +00:00

filter1_test2.bed

More functional test cleanup, eliminated redundant tests, unused test data, and renamed some test data files.

2007-10-04 14:14:15 +00:00

fs-grep.dat

change test data to smaller ones

2007-06-01 20:15:01 +00:00

gops-concat.dat

change test data to smaller ones

2007-06-01 20:15:01 +00:00

histogram_in1.tabular

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

html_file.txt

Some test data I missed.

2007-10-05 19:10:24 +00:00

maf_limit_size1_out.maf

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

phiX.fa

Forgot two test datasets

2008-09-14 14:58:50 -04:00

qualscores.qual454

Added functional tests for testing sniffing and metadata settings of qual454 and qualsolid datatypes.

2009-04-29 16:32:23 -04:00

qualscores.qualsolid

Added functional tests for testing sniffing and metadata settings of qual454 and qualsolid datatypes.

2009-04-29 16:32:23 -04:00

scatterplot_in1.tabular

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

shrimp_cs_test1.csfasta

add shrimp_color_space mapping tool with functional test data.

2008-10-13 15:06:42 -04:00

sort1_alpha.bed

More functional test cleanup, eliminated redundant tests, unused test data, and renamed some test data files.

2007-10-04 14:14:15 +00:00

sort1_num.bed

More functional test cleanup, eliminated redundant tests, unused test data, and renamed some test data files.

2007-10-04 14:14:15 +00:00

taxonomyGI.txt

Changes to taxonomy fetches and two new datatypes: taxonomy and newick

2008-03-04 20:30:26 +00:00