MAF tool interfaces now support the use of index species and all species existing in cached alignment sets.
Until main is updated and the old maf_location files can be overwritten, these symbolic links are required:
maf_index.loc -> /depot/data2/galaxy/maf_index_new.loc
maf_pairwise.loc -> /depot/data2/galaxy/maf_pairwise_new.loc
to set the displayed name of created datasets. This is a template, and can
use the incoming parameters, the tool, and the special "on_string" value
created from the names of the data inputs.
Fixed all references to 'qualityscore' file extensions to be 'qual', since that is the extension in the QualityScore class.
Added functional test to the fastq2fasta converter.
With these notes:
User's can now specify the warnings that they which to report ('nowarns'). There are likely more options but they are unknown.
Using Firefox 1.5.0.12 on Ubuntu with no extensions/addons installed gives me no issues with loading the applet while Javascript is enabled or disabled (works for me).
If a dataset is not the proper format required by a tool, but there is a converter available, the dataset will appear as a valid option in DataToolParameters.
The converted dataset will be created (and subsequently reused) when the job is executed. Conversion utilizes the job runner, and will run on the cluster.
Setting metadata will invalidate the converted dataset, and a new one will be automatically generated as needed.
and tools. Moved some methods related to params out of the Tool class, sets
of inputs can also be used in other ways (e.g. for modules). More abstraction
needed here.
For a multiple select, checkboxes must be used. When not allowing multiple values, radiobuttons must be used.
Options returned from user selections can either be exact, or recursive (the selection of an upper option will result in the passing of all lower options to the command line).
Options can be filtered based upon a metadata key of an input dataset.
Options can also be loaded from a configuration file that exists outside of the tool's xml file.
If javascript is enabled, option hierarchies are expandable and collapsable.
The annotation profiler has been updated to use this parameter type for table selection. See this tool as an example of use.
is "InputDataset" which allows a workflow to have an input dataset which many
different tools can use (without needing to specify it repeatedly. Still need
to extract out a common interface (tools will become another type of "module")
which will clean this up a lot.
properly update the 'terminals' for the nodes in the editor. Many other fixes
to saving and loading of workflows (error tracking should now be working
properly).
Daniel Blankenberg