#!/usr/bin/perl
use strict;
use warnings;

# you can enter as many files as you want as ARGV
while (<>) {
    chomp;
    next if /^\s*$/;  # skip empty lines
    if (rindex($_, "~") != -1) {
    my $number = substr $_, -7, 6;
    print $number ."\n";
    rename $ARGV, $number . ".txt";
    }
} continue {
    close ARGV if eof;  # Not eof()!
}

__END__

$ ls -la | grep txt
-rw-rw-r--  1 user user   78 Dec 15 00:32 in2.txt
-rw-rw-r--  1 user user   78 Dec 15 00:31 in.txt
$ perl test.pl in.txt in2.txt
123456
654321
$ ls -la | grep txt
-rw-rw-r--  1 user user   78 Dec 15 00:31 123456.txt
-rw-rw-r--  1 user user   78 Dec 15 00:32 654321.txt

__DATA__

$ cat in.txt
Line 1 test in file 1
N1*PE*COMPANY NAME INC*XX*123456~
Line 3 test in file 1
$ cat in2.txt
Line 1 test in file 2
N1*PE*COMPANY NAME INC*XX*654321~
Line 3 test in file 2
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