Perl scripting in KNIME


I am starting to use KNIME and want to use perl scripting in my data analysis workflow. I have number of perl scripts which I normally use to do my
analysis. I tried the perl scripting node in KNIME, but I find this node limiting since I have to paste my perlcode in the node. Morover the scripting works on every input row, which is sometimes not really what you want.
I also tried the external tool node, however this node demands an input data file, which I often do not have. Is there an additional way to call external perl scripts with arguments and retrieve the output in the KNIME workflow?



You can use the 'bash' node (in NGS->tools) to execute arbritrary shell commands (including your Perl scripts).

Hello We are trying to use the external tool node to run a perl script. The perl script expects an input argument.  The external tool node gets the input argument from the inject variables node, but uses the variable name and not the value. How can we tell the external node tool to use the value and not the variable?

You need to go into the second tab "Flow Variables" in the dialog and assign the variable to the field you want to control.