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.

Issues:
  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
http://jjohn...@testtoolshed.g2.bx.psu.edu/repos/jjohnson/cummerbund

This includes new datatypes defined in datatypes_conf.xml and implemented in 
cuffdata.py:
      <!-- 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

Thanks,
JJ

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