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

genetrack

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

hyphy

Added functional test for hyphy NJ tree builder.

2010-02-04 11:56:58 -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

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

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

peak_calling

Add a label for experiment name in MACs

2010-02-05 16:27:18 -05:00

plotting

Fix from Assaf Gordon for Cheetah syntax errors in the Bar Chart tool.

2010-02-08 10:00:30 -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

Updated BWA wrapper, SAM to BAM, SAM Merge, and SAM Pileup so that the return code of the program is captured and if it fails, the stderr is printed; temp files are created locally; a message is printed if results file empty.

2010-02-23 10:40:19 -05:00

solid_tools

fix some typos for tools in folders N-Z

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

sr_mapping

Updated BWA wrapper, SAM to BAM, SAM Merge, and SAM Pileup so that the return code of the program is captured and if it fails, the stderr is printed; temp files are created locally; a message is printed if results file empty.

2010-02-23 10:40:19 -05:00

stats

Corrected some typos in DNA filtering tool

2010-02-10 14:59:46 -05:00

taxonomy

Bug fixes to LCA tool

2010-02-22 16:22:12 -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

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