I am attempting to run cuffdiff and have used this tool successfully in the past. For some reason I am seeing unusual behavior in this tool. I have 6 groups with 3 replicates each. When I attempt to add the replicates to each group the drop down menu is populated with all of my accepted hits.bam files from Tophat for all samples. However, when I change the input to allow multiple datasets so that I can load the 3 replicates per group the drop down menu now only allows me to select a subset of all the bam files from Tophat. The scroll bar on the side of each drop down also is not working. I tried re-starting Galaxy and I also tried building a workflow for this but I am still seeing the same behavior. Any help is appreciated.
I apologize, although the behavior of the drop down menu was not as I expected after trying different things I realized that I just need to keep clicking on the vertical scroll bar in order to peruse through all acceptable files. The scroll bar behaves differently than a conventional scroll bar but is functional nonetheless and this was an oversight on my part.
Some tools use the multiple input option in a way that combines files in a single run, others in a way that creates a distinct job for each input. This tool is implemented using the second. Meaning that the job should be run by entering each dataset as a distinct replicate, grouped by condition, on the form (avoiding the multiple input option). Use the "insert condition" and "insert replicate" buttons to expand the options on the form to enter all of your inputs.