Relationship between input and output ports with variables in R scripts. All data items required for analysis and parameterisation are passed into the R script by declaring them as variables named after the input ports. Three input variables have been defined for the RShell processor in example workflow, the 2 sets of microarray data, 'control_csv' and 'test_csv', undergoing t-test analysis and 'pvalue' which defines the threshold used for the t-tests. The results of the R analysis can be passed out into the remainder of the workflow by declaring them as variables named after the output ports. The example RShell processor in the workflow contains only one output, a CSV file containing the differentially-expressed genes identified by the t-tests.