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

Real Job(tm) support for the library upload tool. Does not include iframe upload for the library side yet.

2009-09-25 14:36:12 -04:00

1.axt

Moving james-wsgi branch to new trunk.

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

1.bam

Fixes for Bam data type's set_meta() and sam_to_bam tool, indexes will now be properly created for bam datasets. Fixes also for uploading Bam files, they will no longer be uncompressed on upload.

2009-12-04 19:51:46 -05:00

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.fastq

Added fastq (generic) datatype and deleted fastqsolexa datatype

2009-10-07 12:43:15 -04:00

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.sff

Added sff datatype

2009-11-11 17:55:08 -05:00

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

Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142 .

2009-12-07 10:19:41 -05:00

2gen.fastq

Added fastq (generic) datatype and deleted fastqsolexa datatype

2009-10-07 12:43:15 -04:00

3.bam

Fix for uploading a Bam file that has not yet been sorted, the call to samtools sort has been moved from the sam_to_bam tool to the Bam()set_meta() method to ensure all Bam datasets are sorted prior to indexing. Added new functional tests to cover uploaing unsorted Bam files. Also cleaned up code in the upload tool for uploaing various binary data formats.

2009-12-07 16:04:33 -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

asian_chars_1.txt

Fixes and new functional tests for uploading multi-byte character files and fixes for displaying multi-byte character dataset peek.

2009-10-15 20:10:32 -04:00

cat_wrapper_out1.bed

Modified sort tool to fix backwards compatibility. Reverted catWrapper tool back to old version before recent changes (for backwards compatibility).

2009-09-24 13:54:12 -04:00

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.fasta

First pass of the lastz tool wrapper that includes job splitting - works but needs polishing.

2009-11-27 10:53:50 -05:00

pileup_parser.6col.pileup

Added pileup parser. Pardon the perl = used to its regexes too much

2009-09-04 10:23:37 -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

rgenetics.bed

Update rg test data sample outputs to match the new versions Ross uploaded

2009-11-02 16:52:32 -05:00

rgenetics.bim

Update rg test data sample outputs to match the new versions Ross uploaded

2009-11-02 16:52:32 -05:00

rgenetics.fam

Update rg test data sample outputs to match the new versions Ross uploaded

2009-11-02 16:52:32 -05:00

rgenetics.map

Update rg test data sample outputs to match the new versions Ross uploaded

2009-11-02 16:52:32 -05:00

rgenetics.ped

Update rg test data sample outputs to match the new versions Ross uploaded

2009-11-02 16:52:32 -05:00

sam_to_bam_out1.bam

Fixes for Bam data type's set_meta() and sam_to_bam tool, indexes will now be properly created for bam datasets. Fixes also for uploading Bam files, they will no longer be uncompressed on upload.

2009-12-04 19:51:46 -05:00

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

taxonomyGI.tabular

Rename test files for taxonomy tools and set ftype for test's input datasets.

2009-11-20 15:35:30 -05:00

tinywga.bed

updated rgenetics test files

2009-10-29 17:57:30 -04:00

tinywga.bim

updated rgenetics test files

2009-10-29 17:57:30 -04:00

tinywga.fam

updated rgenetics test files

2009-10-29 17:57:30 -04:00

tinywga.map

updated rgenetics test files

2009-10-29 17:57:30 -04:00

tinywga.ped

updated rgenetics test files

2009-10-29 17:57:30 -04:00