Checking to see if there is any interest in including a parameter option to select outputs for cuffdiff,
potentially including a composite output and a cummeRbund sqlite database.

  cuffdiff produces 21 output files, which is a little unwieldy in a galaxy history.  
  cummeRbund generates its database when given a cuffdiff output directory, but manually hooking up 21 outputs to the cummerbund_wrapper is a pain.

I've put demo code in the testtoolshed under the name repository name cummerbund

This includes new datatypes defined in datatypes_conf.xml and implemented in 
      <!-- html composite dataset with cuffdiff outputs in the extra files path -->
      <datatype extension="cuffdata" type="galaxy.datatypes.cuffdata:CuffDiffData"/>
      <!-- cummeRbund SQLite database -->
      <datatype extension="cuffdatadb" type="galaxy.datatypes.cuffdata:CuffDataDB"/>

The cuffdiff wrapper has a multiple select parameter to choose which output files to put in the history. 
In addition to the 21 cuffdiff outputs, the wrapper can also generate:
  cuffdata - which is a composite HTML output with links to the 21 cuffdiff outputs
  cuffdatadb - which is the cummeRbund SQLite database

I also added utility tools:
  cuffdata_datasets - which will take files from the composite cuffdata and copy them as datasets into the history
  cuffdata_cummerbund - which generates the cummeRbund cuffdatadb from the composite cuffdata

I updated the cummerbund_wrapper:
  with tryCatch so that a R error on a plot won't exit the Rscript
  to include a small image of each plot on the html page
  added plots for : dispersion, scatter matrix, MDS, and PCA