The CS-Rosetta 3.0 (and higher) distribution features a python based toolbox that provides commands for handling and preparation of input files, setting up of rosetta runs and analysis of output.
The toolbox provides a number of applications that help you with translating between formats, preparing and trimming the protein sequence and with picking fragments. All applications provide help with the -h cmdline option. An application reference section is provided here.
A number of tutorials describe how to use the CS-ROSETTA toolbox for structure calculations including the preparation of input files, fragment picking and post-processing.