Thanks Jeremy, that's very helpful, and it's great to hear from a developer!

I have been pursuing option (a), and I feel like I'm very close. The RUM tool 
runs, and the filesizes show up in the history, but the datasets show up as 
erroneous. When I click on the apparently-problematic dataset's bug icon, the 
error message shows the following two lines repeated over 100 times:

yes: standard output: Broken pip
yes: write error

I know what this means, generally, but not in the context of Galaxy. Is this a 
telltale symptom, or is it too generic to say?

Under the additional output, it shows exactly the STDOUT the tool shows when it 
executes and terminates properly from the command line. So I know I'm close, I 
feel like I'm missing something small. 

When I click on the "view dataset button," I see the data, and it's legit. When 
I click "Edit Attributes," I see a message at the bottom of the "Edit 
Attributes" pane that says " Required metadata values are missing. Some of 
these values may not be editable by the user. Selecting "Auto-detect" will 
attempt to fix these values." When I attempt to run the Auto-detect, this 
notification goes away.

It seems like the only issue right now is getting rid of that "broken pipe" 
error message. Once that's gone, perhaps the datasets won't be flagged as 
erroneous and I can use them in downstream processes.

If I can get this tool working perfectly, I'll definitely upload it to the 
Galaxy toolshed.

Any tips you could provide would be greatly appreciated!

Thanks,

Dan

>You have two options:
>
>(a) you can set up the tool to report only a subset of outputs from the tool;
>
>or
>
>(b) you can use a composite datatype to store the complete directory:
>
>http://wiki.g2.bx.psu.edu/Admin/Datatypes/Composite%20Datatypes
>
>Best,
>J.


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