First of all, Thanks!
You are right and the “lefse_res” datatype does not appear when "View data
types registry" .
We had our lefse application which we migrated to the tool_shed.
As part of the migration, we moved the datatypes definition from
to the shed tools in
and it looks in the shed as follows:
<datatype extension="lefse" type="galaxy.datatypes.data:Lefse"
<datatype extension="lefse_res" type="galaxy.datatypes.tabular:LefseRes"
And you can see in the image below that when we run the Lefse program, it
generates output of the type lefse_res.
<param format="tabular" name="inp_data1" type="data" label="Input 1" />
<param format="lefse_res" name="inp_data2" type="data"
does not filter only those datasets?
On Wed, Aug 13, 2014 at 1:33 PM, John Chilton <jmchil...@gmail.com> wrote:
> 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?
> 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
> > 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
> > 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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