If I've reverse engineered a spec from your post correctly, then something along these lines should suffice:

#!/usr/bin/env perl 
use strict;
use warnings;
use feature 'say';

my $infile = shift;
open my $in, '<', $infile or die "Cannot open $infile: $!";
while (<$in>) {
    chomp;
    s/=\s*$/"= " . shift/e;
    say;
}
close $in;

[download]

Running it with your sample input gives:

$ ./bar.pl template.config list.txt file_list.txt
;; path to config file
$;INPUT_FILE$; = list.txt
;; path to list of config files
$;INPUT_FILE_LIST$; = file_list.txt
;; path to temporary directory
$;TEMP_DIR$; = $;TMP_DIR$;
;; use --v for verbose summary
$;OTHER_ARGS$; = --v

[download]

Update: removed a redundant mention of @ARGV in the substitution.

Update 2: for the avoidance of any confusion resulting from the parent post having been rewritten to change both the data set and the invocation, here's the original input file:

;; path to config file
$;INPUT_FILE$; =
;; path to list of config files
$;INPUT_FILE_LIST$; =
;; path to temporary directory
$;TEMP_DIR$; = $;TMP_DIR$;
;; use --v for verbose summary
$;OTHER_ARGS$; = --v

[download]

which was declared to be called as I have above and result in the output which I have also shown above.

In reply to Re: Read in a template file, populate using user input and and generate a new file by hippo
in thread Read in a template file, populate using user input and and generate a new file by Bioinfocoder

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