UPDATE: Update Eoulsan documentation.
UPDATE: Update home page of Eoulsan documentation  by adding "RNA-Seq analysis" and "What's new in Eoulsan" sections.
UPDATE : delete remove R script step in runRserveRnwScript method and
runRnwScript method
Merge branch 'modif' into 1.2
REFACTOR : writeScript become generateScript
REFACTOR : "write" methods are now "generate" methods
UPDATE : in escapeUnderScore method, remove useless split and loop to
use replace method instead
UPDATE : replace inconsistent REngineException by Exception in
runLocalRnwScript method
ADD : enums in DiffAna class for dispersion estimation parameter
FIX : add constant for parameters and fix a wrong test statement
CHANGE : add enum dispersion estimation parameters and change DiffAna
constructor
UPDATE : correct copy paste javadoc error
ADD : parameters for dispersion estimation in DiffAna and parameter to
save r scripts
FIX : documentation markups errors
Merge branch '1.2' into 1.2_DiffanaChanges
UPDATE : document new parameters
FIX : uncomment adding differential analysis step in R script
FIX: In documentation remove in site.xml the links for gmap and gsnap steps.
FIX: In src/site/resources/param-hadoop.xml the --best string in the commented mapping step produced an invalid XML file.
FIX: In src/site/resources/param-hadoop.xml, comment normalization step.