This method only works for single inputs at the moment, though eventually it'd 
be nice to allow pairing.  Another option for you would be to use the workflows 
API, with which you can definitely specify multiple inputs.  See 
workflow_execute.py in the scripts/api folder of your galaxy installation for 
one method of doing this.

-Dannon


On Feb 6, 2012, at 4:53 PM, Dave Lin wrote:

> Thank you Dannon. That is helpful.
> 
>  
> What if I need to specify multiple inputs per run (i.e. .csfasta + .qual 
> file)?
> 
> -Dave
> 
> On Mon, Feb 6, 2012 at 1:27 PM, Dannon Baker <dannonba...@me.com> wrote:
> 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
> 
> <PastedGraphic-2.png>
> 
> 
> 
> 
> 
> On Feb 6, 2012, at 4:18 PM, Dave Lin wrote:
> 
>> Hi All,
>> 
>> I'm looking to batch process 40 large data sets with the same galaxy 
>> workflow.
>> 
>> This obviously can be done in a brute-force manual manner.  
>> 
>> However, is there a better way to schedule/invoke these jobs in batch 
>> 
>> 1) from the UI with a plugin
>> 2) command-line
>> 3) web-service
>> 
>> Thanks in advance for any pointers.
>> Dave
>> 
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