galaxy

annotation_profiler

typo fixes for tools in folders A-M

2009-09-27 23:11:43 -04:00

data_destination

merging from central

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

data_source

Update tool_conf.xml.main and the tool conf for eupathdb.

2010-01-27 08:51:23 -05:00

emboss_5

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

encode

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

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

evolution

Changing an 'and' to 'or' in SNP mutate codon tool error checking.

2009-09-22 11:40:41 -04:00

extract

Added functional tests for a couple of my tools with multiple outputs/pdf outputs.

2010-02-03 13:53:16 -05:00

fasta_tools

Fix fast_compute_length performance by using version contributed by Bjoern Gruning, and fix email configuration bug in the user controller which was found by Ed Kirton.

2010-01-25 10:01:04 -05:00

fastx_toolkit

Fix accidentally committed fastx tool configs

2010-01-07 16:20:04 -05:00

filters

Fixed my previous fix for copying history items to a library, which really didn't fix anything. ¬†Fixed the functional tests for lav_to_bed, split_paired_reads, and solid2fastq by adding the 2nd output dataset to the test for each tool. ¬†Renamed the test files for the tools to have the Galaxy supported file extension.

2010-01-14 09:44:58 -05:00

hyphy

Fixed functional tests for two hyphy tools. The test for the 3rd one (nj tree) with multiple outputs with one of them being a pdf file, has been commented out as it is failing because of the pdf.

2010-02-03 12:21:29 -05:00

maf

Better approach to altering initial content of output dataset if necessary. The upload tool will now call the data type's groom_output_dataset() method ( a better name than before_setting_metadata since it is not related to metadata ). This will now also run on the cluster.

2009-12-08 11:46:13 -05:00

metag_tools

Fixed my previous fix for copying history items to a library, which really didn't fix anything. ¬†Fixed the functional tests for lav_to_bed, split_paired_reads, and solid2fastq by adding the 2nd output dataset to the test for each tool. ¬†Renamed the test files for the tools to have the Galaxy supported file extension.

2010-01-14 09:44:58 -05:00

new_operations

Wiki links now point to bitbucket instead of trac

2010-01-19 18:15:27 -05:00

next_gen_conversion

Fixed my previous fix for copying history items to a library, which really didn't fix anything. ¬†Fixed the functional tests for lav_to_bed, split_paired_reads, and solid2fastq by adding the 2nd output dataset to the test for each tool. ¬†Renamed the test files for the tools to have the Galaxy supported file extension.

2010-01-14 09:44:58 -05:00

plotting

Updating histogram functional test output, which had changed as a result of R version upgrade.

2009-12-14 15:17:13 -05:00

regVariation

Added functional tests for a couple of my tools with multiple outputs/pdf outputs.

2010-02-03 13:53:16 -05:00

samtools

Small edit for the help section

2010-01-14 14:20:01 -05:00

solid_tools

fix some typos for tools in folders N-Z

2009-09-25 02:06:03 -04:00

sr_mapping

Revert bowtie wrapper -- accidently committed change from testing

2010-01-29 11:40:23 -05:00

stats

Added from __future__ import division to the Filter tool and increased the version, and fixed the URL in the new bx_browser tool config.

2010-01-14 11:26:08 -05:00

taxonomy

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

2009-11-20 15:35:30 -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

visualization

Make the GeneTrack datatype binary, containing only the 'indexed' data needed by the GeneTrack server. Better creation of the URL for running the peak predictor tool. \nStill some cleanup/decoupling possible.

2010-02-03 16:33:25 -05:00