You didn't specify on which system the script is running.

• # Outputs file in DOS format.
  # Accepts input files in unix format.
  # Runs on DOS.
  
  {
     my $fh_in = upload('filepath');
     open my $fh_out, ...;
     print $fh_out while <$fh_in>;
  }
  [download]

• # Outputs file in DOS format.
  # Accepts input files in unix format.
  # Runs on unix.
  
  {
     my $fh_in = upload('filepath');
     open my $fh_out, ...;
     while (<$fh_in>) {
        chomp;
        print $fh_out "$_\r\n" 
     }
  }
  [download]

As a bonus, here are more universal versions:

• # Outputs file in DOS format.
  # Accepts input files in unix, DOS and Mac formats.
  # Runs on unix, DOS and Mac.
  
  my $text;
  
  {
     my $fh_in = upload('filepath');
     binmode($fh_in);
     local $/;
     $text = <$fh_in>;
  }
  
  $text =~ s/\015\012?|\012/\015\012/g;
  
  {
     open my $fh_out, ...;
     binmode($fh_out);
     print $fh_out $text;
  }
  [download]

• # Outputs file in local format.
  # Accepts input files in unix, DOS and Mac formats.
  # Runs on unix, DOS and Mac.
  
  my $text;
  
  {
     my $fh_in = upload('filepath');
     binmode($fh_in);
     local $/;
     $text = <$fh_in>;
  }
  
  $text =~ s/\015\012?|\012/\n/g;
  
  {
     open my $fh_out, ...;
     print $fh_out $text;
  }
  [download]

Update: Cleaned up my booboos.

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