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Adjusted subtract_query.py to accomodate for empty fields at end of lines.
Created stable branch.
Added tag release_2013.01.13 for changeset a4113cc1cb5e
merge
Tool stdout/err checking: (a) add tool id to error message and (b) add support for specifying 'both' as an alias for searching both stdout and stderr, which matches the documentation.
Add 'log' level for stdio inspection.
Bugfixes for tool shed functional test scripts.
Allow dynamic_options to use $__user_email__ as a filter_value.  This would enable tools to use dynamic options defined in a file listing user_specific options for a tool (file paths, etc).
Update all template url_for invocations to explicitly specify a controller.  This is preparation for removing the deprecated Routes mapper.explicit option.
Update controller url_for invocations, preparation for enforcing explicit controller specification in the mapper.
Cloudlaunch: During bucket scanning, catch S3ResponseError.  Boto should handle this better in future versions, but for now this can happen if a non-us bucket is accessed.
More url_for changes from base controllers.
Remove 'error' language from debug statement in GalaxyWebTransaction, get_history
Fix MarkupSafe import issue introduced in 7461:5f2db4a18d3d.
history panel: fix to hda update logging typo