> Can it be integrated into galaxy ?

There are no plans to integrate this tool into Galaxy's main server. However, 
should someone outside of the Galaxy team write a patch to integrate this tool 
into Galaxy, they could share it via or community site ( 
http://community.g2.bx.psu.edu/ ) and we would consider adding it to our public 

> I found another tool that does this at http://galaxy.fml.mpg.de/
> Under their SAM tools they have a pileup to wiggle conversion tool 

I'd recommend copying your dataset to the *.de server, performing the 
conversion, and then copying the converted dataset back to the main server.

(Using the 'paste URL' and/or FTP upload option, you should be able to copy 
datasets between Galaxy instances. To copy a dataset between Galaxy servers, 
copy the URL for a dataset from the 'source' server into the upload form in the 
'destination' server and click 'upload')


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