gistfile1.php

/**
 * This script simulates a single sku invoice.
 * It shouldn't be possible via pbridge/payflowpro 
 * but the service_order object allows it
 */

print "Enter orderid: ";
$orderId= trim(fgets(STDIN));

$order = Mage::getModel('sales/order');
$order->load ( $orderId );

// First we prime our shipped items to include 0 units.
foreach ($order->getAllItems() as $item)
    $itemsShipped[ $item->getId() ] = 0;

// Lets ship the first invoice-able item
foreach ($order->getAllItems() as $item) {
  if ($item->canInvoice()) {
    $itemsShipped[$item->getId()] = 1;
    break;
  }
}

// Now lets actually generate the invoice
$invoice = Mage::getModel('sales/service_order', $order)->prepareInvoice($itemsShipped);
if (!$invoice->getTotalQty()) {
   Mage::throwException('Cannot create an invoice without products.');
}

$invoice->setRequestedCaptureCase('online');
$invoice->register();
$invoice->getOrder()->setCustomerNoteNotify(false);
$invoice->getOrder()->setIsInProcess(true);
$transactionSave = Mage::getModel('core/resource_transaction')
    ->addObject($invoice)
    ->addObject($invoice->getOrder())
    ->save();