Hello Len, This is not currently possible in a clean fashion, and providing this feature will take a bit longer than I had originally thought, so I've opened the following ticket for this. You can "follow" the issue in bitbucket if you want. Thanks for sending this. http://bitbucket.org/galaxy/galaxy-central/issue/97/enable-ability-to-have-t... Greg Von Kuster Galaxy Development Team lentaing@jimmy.harvard.edu wrote:

Hi Greg,

We have a program that can either output 1 (a bed file) or 2 files (a bed and a wig file). We'd like to give the user the option to select whether they want 1 or 2 files; in galaxy, is there a way to make the NUMBER of outputs dependent on a variable? I tried this, but it didn't work--when i select "False" for $two_out, galaxy still generates two output files:

... <command interpreter="bash">test_cond_out.sh $output1 </command> <inputs> <param name="two_out" type="select" display="radio"> <option value="true">True</option> <option value="false">False</option> </param> </inputs> <outputs> #if $two_out == "true": <data format="bed" name="output1" /> <data format="bed" name="output2" /> #else: <data format="bed" name="output1" /> #end if </outputs> ...

Thanks,

Len