Processing command line arguments is handled very well by Getopt::Long. The arguments processed by Getopts::Long are removed from @ARGV. Try changing your command line to expect the files to process as the last set of arguments. e.g.
myscript.pl -o output.txt -l log.txt [files to process]

Expanding command line wildcards is either done by the shell (UNIX) or by a module such as Win32::Autoglob for Windows. Failing either of these options, you can also use the glob operator to get an array of filenames.

This example uses Getopt::Long and Win32::Autoglob

#! /usr/bin/perl -w

use strict;

use Win32::Autoglob;
use Getopt::Long;

my $outputFile = '';
my $logFile = '';

my $result = GetOptions ("output=s"   => \$outputFile,
            "logfile=s"  => \$logFile);

print "Output=$outputFile\n";
print "Log=$logFile\n";
$,=' ';
print "Files to work with:",@ARGV;
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