If you can add placeholders [% name %] to your template.config file like this 

[module1]

;;path to speedseq package binary directory
$;SPEEDSEQ_BIN_DIR$; = /usr/local/packages/
;;Sequence file 1
$;Seq1File$; = "[% seq1 %]"
;;Sequence file 2
$;Seq2File$; = "[% seq2 %]"
;;Read Group
$;Read_Group$;='@RG\tID:NA12878\tSM:NA12878\tPL:ILLUMINA\tLB:NA12878\t
+PU:NA12878'
;;Reference
$;Reference$; = "[% ref %]"

[module2]

 ;;Output Chromosome
 $;Chromosome$; = "[% chr_list %]"
 ;;use --v for verbose summary
 $;OTHER_ARGS$; = --v

[download]

then you could use a templating module like Template::Toolkit or Template::Tiny

#!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";

[download]
poj

In reply to Re^3: Read in a template file, populate using user input and and generate a new file by poj
in thread Read in a template file, populate using user input and and generate a new file by Bioinfocoder

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