Also:
- dos2unix test/functional/tools/for_workflows/head.xml
- Single-quote text and data params in `<command/>`
- Remove deprecated `interpreter` attribute of `<command />`
This refactoring is untested and definitely broken in a couple places - but it illustrates broad directions I'd like the work to move in.
- On the input side of things - it serializes the individual parameters to the database each as its own instance of a WorkflowRequestInputParameter. In a couple places I've retried to refactor away from the terminology of "workflow_options" toward resource parameters - there are already other kinds of workflow options.
- On the backend - I've moved a lot of the logic into galaxy.workflow.resources and tried to make it more extensible. The goal is to allow the admin to specify any kind of function to define the parameters as they want for a given workflow and user - but to implement the existing "group based" variant desired by phac-nml as just one potential variant of that with a convient YAML description.
- This moves the priority validation for workflow priorities out of the plugin and handles it up when the request is being handled. This is kind of a hack - but it results in cleaner separation between the DTD and code for defining workflow priorities so that the DTD would work with any potential workflow parameter mapping XML format or dynamic mapping Python function.
- This exposes the workflow parameters to traditional dynamic job destinations (the DTD framework re-computes it from the "job" object and that is fine).
Nate Coraor