Hi Jim, 

> 
> what i mean is, can I get an xml description of all the command line 
> options ?
> 

No, unfortunately not. How do you think this could be useful ?  

>> The only requirement is to prefix input file arguments with the
>> "file:" string, doing that the client takes care to upload them in the
>> scratch folder where T-Coffe will be execute.
> 
> ok. That's good to know - although with Jalview I try to avoid creating 
> files on the client side if possible

I see, but it wouldn't be so difficult to have the client to handle a byte 
buffer instead of a File. 


> 
> Incorporating the client would be a good summer project for a student - 
> want to propose it as a google summer of  code project ?

Yes, it could fit as a google summer project, but quite likely we are already 
going to apply for another project; and also frankly, I think this is more a 
work on Jalview side, so it could have more sense if you apply for it. 


Cheers,
Paolo

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