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Typing just the command by itself will display all possible command line options and parameters.
To extract all the barcode sequences from an .xsq file, use:
extractBCfromXSQ > bc.csfasta 2> bc_QV.qual
To extract all the unassigned F3, or F5-RNA sequences from an xsq file, use:
extractF3fromXSQ > f3.csfasta 2> f3_QV.qual
or
extractF5fromXSQ > f5.csfasta 2> f5_QV.qual
(note that these are all just scripts that call other scripts to do all this - pretty easy to extract anything from an hdf file. You sometimes have to use hdfview to see exactly what the tables in the .xsq file are called, then use h5dump to pull it out).