Checking to see if there is any interest in including a parameter option to select outputs
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 cuffdata.py:
<!-- html composite dataset with cuffdiff outputs in the extra files path
<!-- cummeRbund SQLite database -->
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
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