If you are looking for something to run specific function based on program arguments, like myprog.pl -foo1, you may want to look at the Getopt:: namespace (I like Getopt::Long, but Getopt::Std works for single switches) for argument processing.

Once you have one of the Getopt:: modules working, whichever one, you may want to look at pl2bat (some info here) for making a bat file out of your perl code.

Have you looked at Getopt::Simple or the Getopt::Long

These will handle your script with -a or --a options.

Below is a snippet of an example which came from a Win32 service script.

use Getopt::Long;

my %Config = (
    timeout_value       =>  2,
    log_file            =>  join( "", Win32::GetFullPathName( $0 ) ),
);  

$Config{log_file} =~ s/[^.]*?$/log/;

Getopt::Long::Configure( "prefix_pattern=(-|\/)" );
$Result = GetOptions( \%Config,
                      qw(
                        install|i
                        remove|r
                        timeout_value|t=i
                        log_file|l=s
                        monitor_sub_dirs|s
                        account_id|user=s
                        account_password|pass=s
                        help|?|h
                      ) );
$Config{help} = 1 if( ! $Result || scalar @ARGV );
if( $Config{install} )
{
    Install();
    exit();
}
elsif( $Config{remove} )
{
    Remove();
    exit();
}

if( $Config{help} )
{
    Syntax();
    exit();
}
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You need to parse the command line options (see Getopt::Long) and then run the functions based on that. For instance:

use strict;
use Getopt::Long;

my $a_opt;

my $options = GetOptions('a' => $a_opt);

if($a_opt) { 
  Foo1();
  Foo2();
  Foo3();
}

# Rest of program here
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If you want to run each function separately, put them each into their own script, and run the script from a batch file.

foo.bat:

perl -w foo.pl %1 %2 %3
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foo.pl:

#!/usr/bin/perl -w

# sub foo
{
  my ( $var1, $var2, $var3 ) = @_;

  #  More code follows, using the passed parameters.
}
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That should work.

Update:: Added parameter list on Perl script.