While I was trying to do an example showing Galaxy2, I found myself looking for tools that weren't available. When working with the mutations it would be nice to have some function for getting exact matches, possibly even using the name field. When the data is mixed with very large and very small regions just overlap isn't always to most informative. Mutations also give you up to 3 names for a single nt region. It would take incorporating the name field to distinguish these.
I'm not sure exactly what you mean. Join with the option of matching additional fields? Some kind of filter / match tool that would allow a variable number of input queries could be quite useful. Perhaps the easiest thing to do would be to make a script that does what you want, then integrate it into Galaxy.
Also when it comes to looking at the queries there is nothing for displaying more than 1 at a time. It would be nice to be able to view them as multiple user tracks at UCSC.
Yes, a "build UCSC custom track" tool would be awesome. All of these tools could be built using the multi-page "wizard" tool functionality that is in the framework but not used by many tools. Some modifications would be needed, but it should be straightforward. The idea would be that a tool could provide a "wizard controller" class that would evaluate the current tool state and return the appropriate configuration for the next page or a signal to dispatch to the tool runner. Most of the pieces are already in place.
Also graphs that show more than 1 query? I would have liked somehow either graph or at least a number in a column to be able to get a count of the number of regions that overlapped each region in a second query. Similar to coverage but with counts.
Yes, we've been talking about a tool for progressively building complicated plots for a while. Bob recently expressed some interest in working on this. This could also be a wizard, the fist page would have general plot configuration and from there you would have the option of wither "add another line [pointset, whatever]" or "execute/finish".