Peter has the right idea here - we will add support for appropriate data types 
to the Galaxy distribution.  Of course, the key word here is "appropriate", but 
any industry-standard data format should fall under this category.

On Oct 10, 2011, at 12:46 PM, Peter Cock wrote:

> On Mon, Oct 10, 2011 at 5:09 PM, Duddy, John <jdu...@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
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu




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