Even it is not officially documented it is possible to run target shell scripts from IDE.

How to do it:
Create a normal Qnx Qconn launch configuration. Select ANY project and ANY binary
in the Main page (this is required to satisfy IDE checks, these settings won't be used).
In Upload tab, select "Use executable on target", and type script name (or use browse),
Script must have +x set already. Specify script arguments in Arguments tab. Now you can run it.
It will print output on console. If you want to save output to a file, you can use Common tab to set it.

The other "trick" related to that, if you doing system profiling and your script is a test for already
running processes, you can setup launch configuration for this test script as describe above
but add Kernel Logging Tool to capture the log associated with the test.