Galaxy can sometimes be... confused :). I think Galaxy's database thinks
the datatype is lefse_res - but Galaxy doesn't think that type exists so it
cannot really treat it as a lefse_res when filtering on tools. I think if
you were able to fix the datatype and get it to appear in what Galaxy
perceives as its datatypes things would be working better.

So your datatype definition was:

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

I think this is wrong - perhaps originally you had placed a LefseRes class
in tabular.py but when you move that to the tool shed you need to include a
new datatype file with your types in it. Galaxy's base tabluar.py file
doesn't include a LefseRes class.

So ideally - you would just dynamically subclass an existing type (check
out the emboss_datatypes package in the test tool shed for instance) - but
if you really need to define this LefseRes class in Python than you need to
include its definition with your tool shed entry I think - checkout the
blast_datatypes repository as a good example of this.

Also, there may be more information on the wiki:

https://wiki.galaxyproject.org/ToolShedDatatypesFeatures

Hope this helps,
-John




On Wed, Aug 13, 2014 at 5:11 PM, George Weingart <george.weing...@gmail.com>
wrote:

> 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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>>
>
>
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