I think you can use a flip-flop operator.
#!/usr/bin/perl
use strict;
while (<DATA>) {
print if ( /^input/ ... /\;/ );
}
__DATA__
input CK, n3065gat, n3066gat, n3067gat, n3068gat, n3069gat, n3070gat,
n3100gat, test_si, test_se;
output n3104gat, n3105gat, n3106gat, n3107gat, n3108gat,
n3109gat, n3110gat;
input CK, n3065gat, n3066gat, n3067gat, n3068gat, n3069gat, n3070gat;
[jcua@jcua tmp]$ perl 501.pl
input CK, n3065gat, n3066gat, n3067gat, n3068gat, n3069gat, n3070gat,
n3100gat, test_si, test_se;
input CK, n3065gat, n3066gat, n3067gat, n3068gat, n3069gat, n3070gat;