Thanks for your question.
You are correct in your references to the parameter description and the older thread: majiq psi was intended to be run on a group of replicate samples that, presumably, share the same underlying PSI value. This would be something like cell lines, mouse models, etc. We will work to include this behavior in the Command Builder as an option. In the mean time you can just list out all the .majiq files that you want to be included in your group PSI quantification. For example in Condition_A you would run:
`majiq psi -o ./psi -j 10 -n conda ./build/cond_A_rep1.majiq ./build/cond_A_rep2.majiq`
Currently, the Command Builder output you described is splitting up each sample into its own PSI run. Depending on your samples and experimental design, this may be desirable. For example, if you are dealing with primary human samples were you might expect variability between "replicate" samples that were grouped together at the majiq build step. You may want to compare all replicates against one another within the same group to get an idea of the variability between your group samples, for example.
Let me know if you have any further questions about this or if anything was unclear.