Hi all, I'm in the process of adapting TopHat to our needs, and there are just to many options... It's OK if you run it from the command line, but in Galaxy it looks like a big mess. Similar to Bowtie's tool situation, the "common" option are not specific enough (to our needs) and the "full options" mode is too hard to use (which will result in users not using it at all, or using it wrong). I'd like to request/propose a change in the way the GUI is rendered based on the XML tool. Mainly, to create logical parameter "groups": parameters which logically go together, and are related to one another. In the XML file, it could look like: <inputs> <group name="Introns" help="These settings control the intron sensitivity."> <param name="min_intron_length" type="integer" value="70" /> <param name="max_intron_length" type="integer" value="500000" /> </group> <group name="Quality" help="XXXXXX"> <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /> <param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: /> </group> ... </inputs> And in the HTML output, the groups will be visually distinct, with some nice hide/expand javascript trick, see (fake) example here: http://cancan.cshl.edu/labmembers/gordon/files/galaxy_advanced_options.html IMHO, there are couple of advantages in this layout: 1. The "big-picture" of the available settings is immediately visitble (e.g. "introns", "quality", "segments" etc.). 2. Parameters are separated into logical groups, easier to understand what's being changed (as opposed to one very long cryptic list of parameters). 3. Advanced vs. Simple options are clearly marked 4. Since parameter groups can be hidden, when they are expanded they can contain a help paragraph - this is much easier for the user than scrolling up/down to see the help section below (also - the relevant help section now appears right next to the parameters). I guess this is not a trivial change, but without it it will get harder and harder to integrate complex tools. Comments are welcomed, -gordon