...i am trying to write a shell script that will run 5 of my programs in sequential order.
Are these programs shell scripts, perl scripts, or what?

...however i don't know how to do it so that the input files can be different
I do not quite understand this one.

...i also want to pipe the out put file so that it can be the input file of the next program.
If the 5 programs are perl scripts why not condence them into 5 subroutines included in the same script? ;) If the programs are shell scripts just feed their output into an array and process by passing each value to another subroutine.

Assuming you are taking output from running the other scripts, here is an example of my understanding.

3 scripts: start.pl, hello.pl, and chopup.pl

start.pl

#! /usr/bin/perl -w
use strict;
my @program1 = `perl ./hello.pl`;
foreach (@program1) {
  # pass to program2
  &program2($_);
}

sub program2() {
  # value from program1
  my $value = shift;
  my @newvalue = `echo $value | perl ./chopup.pl`;
  foreach (@newvalue) {
     print $_;
   }
}
[download]

hello.pl

#! /usr/bin/perl -w
use strict;
my $message = "Hello Lucy!";
print "$message";
[download]

chopup.pl

#! /usr/bin/perl -w
use strict;
chomp (my $value = <STDIN>);

my @value = split "",$value;
my $count = @value;

my $i;
for ($i=0;$i<$count;$i++) {
  print "\@value[$i] = $value[$i]\n";
}
[download]

Run ./start.pl and all files will be processed. I hope this helps, or maybe I should say I hope my understanding is correct! ;