~$:/path/executable

"Here is the script. Please choose option 1 or 2"

1

"Thank you. Please provide the input file name:"

myInputFile.txt

(script runs and output file appears in the directory)
~$:

##</code><code>##

#I have tried
my $program = "path-to-executable";
system($program); #The script hangs here until I manually enter the requested info at the command line
system("1");
system("myInputFile.txt");

#Have also tried
my $program = "path-to-executable";
my $i = `$program`; #Script hangs here and nothing appears on the command line at all
$i = `1`;
$i = `myInputFile.txt`;