galaxy

annotation_profiler

Resync Annotation Profiler tests to current cached data.

2010-06-02 16:40:39 -04:00

data_destination

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data_source

Remove link target from intermine datasource tools.

2011-03-22 20:29:32 -04:00

discreteWavelet

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

emboss_5

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

encode

Fix gencode partition tool to not use hard-coded paths.

2009-12-09 15:21:41 -05:00

evolution

Fixes to aaChanges tool

2010-12-02 13:04:05 -05:00

extract

Fix bug in extract_genomic_dna to handle non-GFF files when interpret features is true. Tweak functional test to cover new behavior.

2011-02-16 21:46:23 -05:00

fasta_tools

Fix typo in fasta/fastq to tabular converters

2010-12-10 16:29:03 -05:00

fastq

Add more verbose error reporting to FASTQ Groomer tool.

2011-03-24 11:45:50 -04:00

fastx_toolkit

Update FASTX tool wrappers to handle fastqsanger by passing -Q 33 to command-line as needed.

2011-01-27 09:54:53 -05:00

filters

fixed calculation of codon starts

2011-03-24 15:03:12 -04:00

genetrack

Add bed6 and bed12 datatypes, which are subclasses of bedstrict; converters are available to turn any interval datatype into these types. Change GeneTrack Indexer tool and converter to use bed6 as input.

2010-04-01 13:08:48 -04:00

human_genome_variation

fixed comment bug and added additional error messages for SIFT tool

2011-03-22 13:45:31 -04:00

hyphy

Added functional test for hyphy NJ tree builder.

2010-02-04 11:56:58 -05:00

indels

Remove imports of the sets module, set has been a standard type since 2.4. There are more in tools, but they check for the existence of set() first, so will not raise a warning.

2010-09-27 21:35:03 -04:00

maf

Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.

2011-02-28 12:16:28 -05:00

meme

Update test-data files for meme 4.6.0

2011-02-25 14:58:35 -05:00

metag_tools

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

multivariate_stats

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

mutation

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

ncbi_blast_plus

BLAST test changes

2011-04-04 12:55:33 -04:00

new_operations

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

next_gen_conversion

Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.

2011-02-28 12:16:28 -05:00

ngs_rna

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

ngs_simulation

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

peak_calling

Update CCAT to version 3.0.

2011-03-16 10:41:38 -04:00

plotting

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

regVariation

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

rgenetics

change to weblogo test jpg comparison and code cleanups to rgCaCo

2011-04-05 14:07:10 -04:00

samtools

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

solid_tools

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

sr_assembly

Convert a bunch of binary requirement tags to package requirements, and change the sputnik tool to call 'sputnik' instead of 'bx-sputnik'.

2010-10-07 16:23:57 -04:00

sr_mapping

Set the ftype of SRMA test outputs so the BAMs are compared as SAMs

2011-03-23 10:59:26 -04:00

stats

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

taxonomy

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

validation

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vcf_tools

Fix for vcf_extract tool test

2011-03-02 09:40:10 -05:00

visualization

Create NGS peak calling section. Add MACS peak caller. Move GeneTrack to new section. Increment sam2interval tool version.

2010-02-05 16:06:27 -05:00