In your workflows, are you using "Input Dataset" steps?  Galaxy uses these 
steps to know how to map datasets to do special things like this.  If you're 
not currently using them, just open the workflow editor and add input dataset 
steps (it's at the very bottom of the tool list) connected to the tool inputs 
at the highest level of the workflow, and you'll see the multiple dataset 
flagging when you go to run it next time.

-Dannon

On Jul 4, 2012, at 3:19 AM, Bernd Jagla wrote:

> Dannon Baker <dannonbaker@...> writes:
> 
>> 
>> Hi Dave,
>> 
>> Yes, galaxy's standard run-workflow dialog has a feature where you can 
>> select 
> multiple datasets as input
>> for a single "Input Dataset" step.  To do this, click the icon referenced by 
> the tooltip in the screenshot
>> below to select multiple files.  All parameters remain static between 
> executions except for the single
>> input dataset that gets modified for each run, and that only one input 
>> dataset 
> can be set to multiple files
>> in this fashion.
>> 
>> -Dannon
> 
> Dannon,
> 
> what if I don't have this icon??? How can I enable this? Where is this 
> documented?
> 
> Thanks,
> 
> Bernd
> 
> 
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