[galaxy-user] File extensions

One issue I have stumbled upon is that the tmp files fed into the program do not preserve the file extension attributed to the type of file (.bam, .fastq, .fasta) but instead use ".dat". Is there a way to force this, as tools that I am trying to wrap require the file extension to be present. Also, is there a way to model a map reduce style workflow in Galaxy. Say I have a fastq splitter that splits the fastq file into 100 pieces, then I want to run a process on each piece, then finally merge the results (3 tools, one workflow). Since Galaxy can submit to SGE/PBS/etc this would be extremely useful for cluster users (or cloud users). Is this possible? Nils