On Mon, Oct 10, 2011 at 5:09 PM, Duddy, John <jduddy@illumina.com> wrote:
I agree with the risks you cited.
There is a risk in the other direction that I think is even scarier - without the ability to add data types, tool authors may be forced to use a "typeless" system, declaring all inputs/outputs as "data" or "text". While this works, it has the same drawbacks as typeless programming languages - deferring error detection to runtime, impairing the ability to perform static analysis, inability to perform transparent type conversions - in other words, the tools have to take over responsibilities from the framework.
Like all interesting problems, I don't think there is an "obviously right" answer ;-}
John Duddy
Indeed. I'm going with lobbying the Galaxy to include new datatypes when I need them (InterProScan XML in on my todo list, perhaps v4 and v5 as two types), but I've been able to get a long with with "tabular" as a tool output. Peter