CummeRbund is an R package that is designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output.
( http://compbio.mit.edu/cummeRbund/ )  
( http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html )


Prerequisites for installing cummeRbund:
The linux package: libxml2-dev
In ubuntu:   sudo apt-get install libxml2-dev

R package: ggplot2
   install.packages("ggplot2",dependencies = TRUE)

To install cummeRbund on your R server, follow the directions in:
( http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html )
   source("http://bioconductor.org/biocLite.R")
   biocLite("cummeRbund")

This galaxy tool package includes a replacement variation of the cuffdiff wrapper that will generate an SQLite data base output that can be used directly in cummeRbund.
This cuffdiff builds the cummeRbund database from the cuffdiff output files in the working directory which includes the run.info output, 
thus it can populate the replicates information.