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 server.
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')
Thanks, J.