I would also like to voice my support for this feature. I wrote a wrapper for bowtie that converts the SAM output to BAM after bowtie is finished just to avoid the hassle of letting galaxy "know" that the SAM file existed (didn't want to run Tophat).

After thinking about how I would go about deleting an existing output it occurred to me that a "deleting tool"  would require some extra logic since you would probably want to prevent the output port on a workflow node/tool from being connected to the input of another node if the output is going to be deleted. 

I was wondering if it might make sense to modify the "flagged output" feature (the asterisk) of the galaxy tools nodes to delete the non-flagged outputs instead of just hiding them? Or perhaps just mark them as deleted so they will be taken care of by the cleanup scripts?

 In this same line of thinking, it might make sense to have a flag for the input ports that specify that the input will be consumed/deleted after the tool has successfully run. This would address the case where you wanted to use the output of a tool before it is removed.

Cheers,

Andrew