Hi John,

First of all, Thanks!

You are right and the “lefse_res”  datatype does not appear when "View data
types registry" .

However:

We had our lefse application which we migrated to the tool_shed.

As part of the migration, we moved the datatypes definition from
//usr/local/galaxy-dist/datatypes_conf.xml
 to the shed tools in

/usr/local/shed_tools/
testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/47ac77f2fe68/lefse/datatypes_conf.xml

and it looks in the shed as follows:

<?xml version="1.0"?>

<datatypes>

   <registration>

   <datatype extension="lefse" type="galaxy.datatypes.data:Lefse"
display_in_upload="true"/>

   <datatype extension="lefse_res" type="galaxy.datatypes.tabular:LefseRes"
display_in_upload="true"/>

   </registration>

</datatypes>

And you can see in the image below  that when we run the Lefse program, it
generates output of the type lefse_res.

So why

<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>

does not filter only those datasets?

Thanks!!

George





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?
>
> -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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