Hi Anon Monk!
I encourage you to sign up for an account. An account is free and helps at least me understand who is posting what...

I found your code hard to follow. I present an alternative below and will offer a few comments.

• I have no comments about the command line and Get::Opts. My code starts with a list of files to process.
• The use of array subscripts is rare in Perl. My code below does have one such use to index the translation of a number into a string representing the day of week.
  Your code has an inappropriate and I think an incorrect use. for(my $i=1; $i < scalar @files; $i++) I think $i=0 would be correct. But in any event, in Perl use a foreach iterator over an array.
• Instead of complicated flags like if($firstline==1){}, call a subroutine to deal with the first line.
• Then setup a loop to process the 12 line chunks. I show a very standard way to do this. process_one_minute() will be called repeatedly until there a no complete 12 line chunks left.
• I am sure that there are some formatting and spacing issues with the printout.
• But I hope that his helps..
Some Code:

#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;
use Date::Calc qw/Date_to_Time/;

my @files = ('FiveSecondSamples.txt');
my @weekDay_text = qw(Sun Mon Tue Wed Thu Fri Sat); 

####  This is the Main Loop..., note that the main loop is "short"

foreach my $in_file (@files)
{
    open my $fh_in,  '<', "$in_file" or die "unable to open $in_file $
+!";
    open my $fh_out, '>', "$in_file"."_outfile.txt" or die 
                          "unable to open outfile for $in_file $!";
   
    # deal with the special first line 
    #
   
    my $current_time = process_header_line( $fh_in, $fh_out);
   
    # process the data in one minute chunks (12 samples per minute)
    #
   
    while ($current_time = process_one_minute($fh_in, $fh_out, $curren
+t_time)){};
}

####
####  The Main Loop is "over", now subroutines in the code...
####

## Process the input header line for start time and setup the output h
+eader
#
sub process_header_line
{
    my($fh_in, $fh_out) = @_;
   
    my $first_line = <$fh_in>;
    print $fh_out "#$first_line"; ### debug ## first input line as com
+ment
   
    my ($year1,$month1,$day1,$hour1,$min1,$sec1,
        $year2,$month2,$day2,$hour2,$min2,$sec2,) = $first_line =~ /(\
+d+)/g; # with caveats
   
    my $start_time = Date_to_Time($year1,$month1,$day1,$hour1,$min1,$s
+ec1);
   
    print $fh_out "Date\t\tTime\t\tDay\tmg\n";    # print output file 
+title line
   
    return $start_time;
}

## Process each minute of data (12 samples)
## A block of data with less than 12 samples is not processed
#

sub process_one_minute
{
   my ($fh_in, $fh_out, $current_time) = @_;
   
   my $total = 0;
   
   for (1..12)
   {
       my $in = <$fh_in>;
       return 0 unless defined $in; # No output if <12 samples in this
+ set.
                                    # This the "eof, "file empty" retu
+rn, 
                                    # no more complete sets of 12 samp
+les
       
       my ($num) = split(',',$in);
       $total += $num;
   }
  
   my $avg = $total/12;
   $current_time += 60;  # add 60 seconds to the "epoch time"
   
   my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) =
                                                gmtime($current_time);
   
   printf $fh_out "%d-%02d-%02d\t%02d:%02d:%02d", 
                  $year+1900, $mon+1, $mday, $hour, $min, $sec;   
   print $fh_out "\t",$weekDay_text[$wday];
   print $fh_out "\t$avg\n";
   
   return $current_time;   
}
[download]

The Input:

acceleration (mg) - 2013-10-09 10:00:00 - 2013-10-16 09:59:55 - sample
+Rate = 5 seconds,    imputed
46.3,    0
17.1,    0
30.1,    0
38.4,    0
97.1,    0
87.3,    0
84,    0
78.5,    0
67.9,    0
83.5,    0
155,    0
103.5,    0
[download]

The Output:

#acceleration (mg) - 2013-10-09 10:00:00 - 2013-10-16 09:59:55 - sampl
+eRate = 5 seconds,    imputed
Date        Time        Day    mg
2013-10-09    10:01:00    Wed    74.0583333333333
[download]

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