Maybe you could use Expect (untested):

use warnings;
use strict;
use Expect;

my $command = 'path-to-executable';
my $exp = Expect->new();
$exp->raw_pty(1);  
$exp->spawn($command)
    or die "Cannot spawn $command: $!\n";
$exp->send("1\n");
$exp->send("myInputFile.txt\n");
$exp->soft_close();
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