The (error) messages i get are warnings, like "use of uninitialised variable at some place"

That's not the exact error message. Don't give a vague description of what it's like. Tell us exactly what it is. Then show the code around it.

To do that I created a perl environment in Tcl and used the open command to call my .pl file.

That sounds reasonable, except that the code that you've posted isn't (as far as I can tell) valid Tcl code. I expect something closer to:

set my_perl [open "|perl perl_file.pl $variable1 $variable2"]
...
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I provided this code snippet so as to confirm that the way with which I'm passing parameters from tcl to perl were correct.

We'd have to see a lot more code, including the Perl program -- at least how it expects to access incoming parameters.