galaxy

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

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

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

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

Have Extract Genomic DNA tool copy metadata from input file.

2009-11-16 10:57:31 -05:00

fasta_tools

Fixed for functional tests for new version of fasta_filter_by_length tool contributed by James Casbon.

2009-07-23 14:31:11 -04:00

fastx_toolkit

Modified test data and tool conf for fastq stats

2009-10-08 14:50:28 -04:00

filters

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

hyphy

typo fixes for tools in folders A-M

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

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

Upgrade to Cheetah 2.2.2

2009-11-10 13:47:34 -05:00

new_operations

Fixed a bug in 'fetch closest features' tool.

2009-11-30 11:59:54 -05:00

next_gen_conversion

Updated solid_to_fastq so that -1 qualities are converted to 1 before conversion to FASTQ.

2009-10-21 16:04:24 -04:00

plotting

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

regVariation

When setting metadata externally, substitute a MetadataTempFile object for all populated metadata FileParameters. Fixes the problem with writting to metadata FileParameter files on cluster nodes with read-only database/files directory.

2009-11-30 14:55:30 -05:00

samtools

Rename the before_edit() and after_edit() metadata related methods to be more appropriately named before_setting_metadata() and after_setting_metadata(), and add the metthods to all datatype classes. Move sorting of Bam files from the Bam set_meta() method to this new method.

2009-12-08 09:05:35 -05:00

solid_tools

fix some typos for tools in folders N-Z

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

sr_mapping

Changed Lastz call for tabular (general) format to suppress header

2009-12-07 15:57:06 -05:00

stats

Upgrade to Cheetah 2.2.2

2009-11-10 13:47:34 -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

Fix most of the db flushes to be compatibel with sqlalchemy 05. Add the _monkeypatch_query_method() back into assignmapper due to a single object.get() method in the MetadataCollection class since Metadata has no current hook into mapping.context ( the sqlalchemy session ). There a 4 flushes in metadata,py and 20 flushes in model.__init__.py that still use the _monkeypatch_session_method in assignmapper due to the same issue, but all other flushes are fixed.

2009-11-11 15:59:41 -05:00