If you're confident about the format of the dataset in question, add a Change 
Datatype action to your workflow (on the step before bowtie) that sets the 
datatype to fastqsanger.  

See the right panel of the workflow editor under Step Actions; you want 
something like this:

<<inline: PastedGraphic-4.png>>



-Dannon


On Feb 9, 2011, at 10:58 AM, Jeremy Goecks wrote:

> Steve,
> 
> I'm sending this question along to the galaxy-user list because it's likely 
> of interest to others as well as yourself. Dannon, our resident workflow 
> expert, should be able to answer your question.
> 
> Thanks,
> J.
> 
> 
> 
> On Feb 9, 2011, at 10:28 AM, Stephen Taylor wrote:
> 
>> Hi,
>> 
>> I seem to remember sending a question about how to change the type of fastq 
>> in a workflow to the galaxy-dev list so it can run vs bowtie without going 
>> through fastqgroomer. I think you replied to me about a tool that would do 
>> this but I can't seem to find the answer on the list or in my inbox? Is 
>> there a way to to do this or did I dream the question/answer?!:-)
>> 
>> Kind regards and thanks,
>> 
>> Steve
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
> 
> 
> _______________________________________________
> galaxy-user mailing list
> galaxy-user@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-user

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