Hi,
We are getting multiple requests for this but did not have the bandwidth to do it. So if you are planning to implement - share through the toolshed and we will roll it to main.
The way I got round this was let the SRA website do the conversion. So just paste in the URL in the upload screen:
http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=dload&run_list=SRRX...
Where SRRXXXXXX is the archive of interest, and it downloads Sanger FASTQ sequences to Galaxy.
Regards,
Steve