I am not sure about cuffcompare, but cuffdiff doesn't generate any extra files if you add more groups and replicates to the command line. It adds columns to the output files but the number of files remains the same.
Hmm. This is a new and welcome change.
For a workflow for Martin for now, I would suggest doing this for making calls with no novel genes:
1) upload your reads 2) fastq groom them into sanger format 3) run tophat on each lane individually 4) run cuffcompare with the gtf file you downloaded from uscs or wherever against itself, this puts it in a nice format to use with cuffdiff 5) merge the bam files from tophat for the 10 lanes from each group into one file 6) run cuffdiff using the transcript gtf output file from cuffcompare and the two merged bam files
You can also run this workflow easily enough for de novo transcripts as well; only change is whether Cufflinks is fed a reference GTF.
I have patched galaxy to have cuffdiff handle replicates and to do normalization, when that gets merged into the main branch your workflow will be the same except you won't have to merge all of the bam files from each condition together to use cuffdiff.
Yes, looking into this soon. J.