Haklısın. Biraz araştırınca benzer örnekleri aşağıda vermişler.
Şimdilik ben çözümü buldum ama arayan varsa aşağıdaki kodu örnek alabilirler.

Mesela

<?php 
#code for pdf to swf using pdf2swf software 
#this codeworks in windows environment. 
  

## Important Parameters 
$software_path  ="C:\\SWFTools\\pdf2swf" ; 
$pdf_path       ="C:\\SWFTools\\abcd.pdf" ; 
$argument       = "-o"; 
$swf_output     ="C:\\SWFTools\\abcd.swf" ; 

  

#actual code 
$cmd        =" $software_path $pdf_path  $argument $swf_output"; 

$WshShell   = new COM("WScript.Shell"); 
$oExec      = $WshShell->Run("cmd /C $cmd ", 0, true); 

# 0 for command prompt invisible mode 
# 3 for visible 

?>