When Galaxy cannot find the extension/short name corresponding to a
datatype it treats the input as a 'data' the root datatype meaning
anything can connect to it. So I think the problem here is not so much
your tool format as your datatype - I don't think Galaxy can see the
lefse_res datatype. You could try to confirm this by swapping the
order of the inputs I think.

Can you go to the "View data types registry" option in the admin menu
and see if Galaxy thinks it knows about this datatype?

-John

On Wed, Aug 13, 2014 at 2:56 PM, George Weingart
<george.weing...@gmail.com> wrote:
> Hi,
>
>
> I am trying to set up in our Galaxy a program that takes two inputs that
> have different datatypes.
>
> The problem is that Galaxy selects only datasets of the first datatype and
> displays all datasets for  the second with all types, not only with the
> specified datatype (We want it to display for the second dataset only those
> with datatype=”lefse_res”).
>
>
> Both datasets are input and are both required to run the step.
>
>
> My code looks as follows:
>
>
> <inputs>
>
>  <param format="tabular" name="inp_data1" type="data" label="Input 1" />
>
>            <param format="lefse_res" name="inp_data2" type="data"
> label="Input 2"/>
>
> </inputs>
>
>
> Should I be doing it in another way?
>
> Thanks!
>
> George Weingart
>
>
>
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