#!perl
use strict;
use Getopt::Long;
use Template;

my $msg = qq! perl $0 template.config 
  --seq1 USER_INPUT.txt     --Seq2 USER_INPT2.txt 
  --Ref  USER_INPUT_REF.txt --chr_list USER_INPUT_CHR.txt!;

my @options = qw(seq1=s seq2=s ref=s chr_list=s); # strings
my $vars={};
GetOptions ($vars,@options)
 or die ("Error in command line arguments\n");
 
# check for all options
my $input  = $ARGV[0];
die "$input not a valid template" 
     unless $input =~ /config/; # validate as req
for (@options){
  my @f = split '=';
  die "$msg" unless exists $vars->{$f[0]}; 
}

# create new template
my $output = 'new_'.$input;
my $tt = Template->new();
$tt->process($input,$vars,$output) 
  or die $tt->error(), "\n";

print "$output created\n";