galaxy

2011-04-13 21:02:06 +02:00

2008-10-28 11:28:15 -04:00

Uploading a compressed library dataset using either the server directory or path paste methods was previously overwriting the input file, which should never happen. This changeset also makes it possible to upload compressed files that remain compressed (by choosing to "link files only"), however, Galaxy does not yet open the compressed file to properly set metadata on its contents.

2011-06-08 15:35:36 -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

Enable GFF filter attributes tool to accept arbitrary conditions.

2011-05-05 16:51:56 -04:00

gatk

Have GATK file listings written as html, be sorted.

2011-05-12 12:13:18 -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

genome_diversity

Updated help text for genome diversity tools

2011-05-27 09:22:27 -04:00

human_genome_variation

Updated Freebayes to set dbkey on output file

2011-05-09 16:40:44 -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

Update tool help for some MAF tools.

2011-05-17 12:07:25 -04:00

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

Fix for BLAST XML to tabular when both query and subject have XXX masking

2011-05-18 18:43:46 +01:00

new_operations

Make gops subtract tool compatible with GFF features rather than lines.

2011-05-03 11:35:21 -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

Rename and reorder Cuffdiff outputs for clarity.

2011-06-07 14:31:35 -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

Have MACS peak caller wrapper use return code to set error state.

2011-05-10 10:50:26 -04:00

picard

Fixes to picard tool intefaces and help sections. Disabled java heap selection by the user (set to 4G default, which was changed in picard_wrapper.py).

2011-05-20 13:26:45 -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

Cleaned up help text across Picard tools (and FastQC) to standardize style as much as possible

2011-05-17 21:31:34 -04:00

samtools

Updated sam-to-bam to properly assign output dbkey; enhanced sam-to-bam and bam-to-sam functional tests

2011-05-09 12:00:05 -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

Velvet wrapper: fix typos, tabs -> spaces, spacing

2011-05-27 11:01:46 +02:00

sr_mapping

Updated help section of BWA wrappers to include tags for the RG header record type

2011-05-12 13:38:00 -04:00

stats

Improve docs for Grouping tool. Closes #576

2011-06-06 15:30:02 -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

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

vcf_tools

Fix for vcf_extract tool test

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

visualization

fixed some configuration files

2011-04-13 21:02:06 +02:00