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.bed

change test data to smaller ones

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

1.bed.spaces

Bug fix for handling 'spaces to tab' for non-binary composite datatype files.

2010-06-07 15:34:20 -04:00

1.bedgraph

Enable BedGraph to be used as input to wig-to-bigwig tool.

2013-01-24 17:06:51 -05:00

1.bigbed

Apply patch from Brad Chapman providing support for detecting, uploading and displaying UCSC bigWig and bigBed. Add new functional tests for uploading and detecting bigbed and bigwig formats, and correct and clean up the test_get_data.py functional test script.

2010-08-19 13:58:10 -04:00

1.bigwig

Apply patch from Brad Chapman providing support for detecting, uploading and displaying UCSC bigWig and bigBed. Add new functional tests for uploading and detecting bigbed and bigwig formats, and correct and clean up the test_get_data.py functional test script.

2010-08-19 13:58:10 -04:00

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.pileup

Added new tabular/pileup join tool and associated test files. Also added pileup datatype.

2010-03-26 12:00:55 -04:00

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.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.bz2

Add test for bz2 file upload

2010-09-10 14:17:05 -04:00

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

4.bed.zip

Removed binseq.zip test and replace it with a zip test.

2010-07-01 08:59:26 -04:00

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 the qual_stats_boxplot and quality_score_distribution tests again, hopefully

2011-03-02 13:46:07 -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

empty_file.dat

Add a new FASTQ tool suite. Four FASTQ variants are supported: sanger, illumina, solexa and solid.

2010-02-23 16:48:07 -05:00

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_in3.sam

Enable filter tool to operate correctly on files with a variable number of columns (such as SAM files). Tool prepares and processes only columns up to and including the right-most column (i.e. column with the largest index) in the filtering condition, and subsequent columns are ignored. New functional test added for this functionality as well.

2010-11-04 16:30:34 -04:00

filter1_in5.tab

Add parameter to filtering tool to optionally skip header lines. Add test for new parameter usage as well.

2013-01-29 10:37:16 -05:00

filter1_inbad.bed

[Peter Cock] Filtering tool: Only cast used columns. Fix valid lines and skipped info lines. [Kanwei] Add new testcases to test this behavior. Fixes #537 . Fixes #535

2011-05-27 10:47:17 +02:00

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

filter1_test3.sam

Enable filter tool to operate correctly on files with a variable number of columns (such as SAM files). Tool prepares and processes only columns up to and including the right-most column (i.e. column with the largest index) in the filtering condition, and subsequent columns are ignored. New functional test added for this functionality as well.

2010-11-04 16:30:34 -04:00

filter1_test4.bed

[Peter Cock] Filtering tool: Only cast used columns. Fix valid lines and skipped info lines. [Kanwei] Add new testcases to test this behavior. Fixes #537 . Fixes #535

2011-05-27 10:47:17 +02:00

filter1_test5.tab

Add parameter to filtering tool to optionally skip header lines. Add test for new parameter usage as well.

2013-01-29 10:37:16 -05:00

fs-grep.dat

change test data to smaller ones

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

gops_concat_out1.bed

Enhance functional test framework so that a boolean form field ( checkbox ) can have a false value ( be unchecked ). Add a 2nd test to gops_concat that uses this behavior.

2010-02-17 11:07:08 -05:00

gops_subtract_in1.gff

Add GFF support to GOPS subtract tool and updated functional tests. Using the GFF-->BED converter is lossy as GFF has more attributes/features than BED, so it's necessary to directly support GFF. Basic approach used is to modify interval coordinates during reading and writing while not changing the middle, computational steps; this approach can be used to provide GFF support for any tool that uses bx-python to operate on intervals.

2010-06-07 16:28:46 -04:00

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

paired_end_1_singles.fastqsanger

Add missing test files

2011-06-10 20:10:09 -04:00

paired_end_2_singles.fastqsanger

Add missing test files

2011-06-10 20:10:09 -04:00

paired_end_merged_singles.fastqsanger

Add missing test files

2011-06-10 20:10:09 -04:00

phiX.fasta

Converted several tools to data table style of loc file handling (Bowtie, BWA, Lastz, Megablast, PerM, SRMA). Cleaned up several tool XML files, removing unnecessary None parameters.

2010-11-08 00:10:13 -05:00

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

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

tinywga.ped.space_to_tab

Bug fix for handling 'spaces to tab' for non-binary composite datatype files.

2010-06-07 15:34:20 -04:00