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 <jmchilton@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
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
On Wed, Aug 13, 2014 at 2:56 PM, George Weingart <george.weingart@gmail.com> wrote: 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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