Greg Von Kuster bbba08b89d Gzipped files from UCSC will now be decompressed on the fly. Also fixed a bug in biomart_filter.

2007-12-10 16:13:05 +00:00

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data_source

Gzipped files from UCSC will now be decompressed on the fly. Also fixed a bug in biomart_filter.

2007-12-10 16:13:05 +00:00

emboss

Changing all tools that use 'text' as file extension to now use 'txt'. We are eliminating the use of 'text' as a file extension within Galaxy and will now use only 'txt' for Text data types.

2007-09-27 12:24:27 +00:00

encode

Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return.

2007-11-21 18:48:37 +00:00

extract

More dynamic options cleanup. Eliminated the "tool_type" attribute, among other cleanup chores.

2007-11-30 20:08:21 +00:00

filters

More MAF tools now have better behavior when no species are selected.

2007-11-29 18:13:48 +00:00

hyphy

Adding HYPHY tool to compute dN/dS ratio.

2007-07-11 20:05:20 +00:00

new_operations

Bug fix in subtract_query1, made CustomTrack.sniff() more restrictive.

2007-10-30 13:28:24 +00:00

patmat

Changing all tools that use 'text' as file extension to now use 'txt'. We are eliminating the use of 'text' as a file extension within Galaxy and will now use only 'txt' for Text data types.

2007-09-27 12:24:27 +00:00

plotting

More ColumnListParameter cleanup. Eliminated dynamic options from some tools by using ColumnListParameter.

2007-10-18 17:29:47 +00:00

regVariation

Uncommented functional tests in some regVariation tools in preparation for moving them to main.

2007-11-30 13:43:59 +00:00

stats

Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return.

2007-11-21 18:48:37 +00:00

validation

Cleanup: removing the cookbook package. Bunch and odict move to galaxy.util, tools

2007-07-31 15:45:59 +00:00

visualization

Fix for building custom tracks from interval files.

2007-11-10 01:32:19 +00:00