use v5.16;
use strict;

my $prBoundaryString = <<endPrBoundary;
'( (0.01 0.02) (0.0 1328.23) (0.01 0.02) (0.04 0.53) (0.03 44.23)
   (0.0 1328.23) (0.04 0.53)
 )
endPrBoundary

say "prBoundaryString=$prBoundaryString";

my @pts = grep { /\d+/ } split /\s+|[()]/, $prBoundaryString;

my $count = 0;
for ( 0 .. $#pts ) {
    if   ( $_ % 2 == 0 ) { print qq[-x$count=$pts[$_]] }
    else                 { print qq[-y$count=$pts[$_]]; $count++ }
}