For what it's worth (not much ;), I think the dataset naming is the single least intuitive part of the galaxy system for biologists.

I think there's a proposal to "fix" this problem - and mainain the connection between input data set and derived data, but It doesn't seem to have gone anywhere yet. 

Anyway, you have to check the name of the field for each tool - it's sometimes "input" and sometimes something else.

You want to use the #{} for naming.  The ${} stuff is for parameters

I also do this kind of thing: to keep the names from getting too long.

#{input_1 | basename}.bam

The basename removes everything after the last . character.

Brad