I'm not quite clear exactly what you are trying to do, but if it is all possible, you should (in general) avoid calling shell scripts (and other non-portable commands) in your perl scripts. Instead, where possible, use modules that provide equivalent behavior.
That being said, you can easily run shell commands using the back-ticks operator
`echo "blah"`, or the regex like quote operators
qx{echo "blah"}. Output to STDOUT from the shell command is returned.
If that doesn't answer your question, perhaps you could clarify a bit, or post some example code?
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