vat_breakdown.php

  // VAT BREAKDOWN:
  $header = array(
    t('VAT -%'),
    t('Net'),
    t('VAT'),
    t('Gross'),
  );
  // First, product:
//  $line_item_wrapper = entity_metadata_wrapper('commerce_line_item', $line_item);
//  $price = $line_item_wrapper->commerce_total->value();
//  $base_price = commerce_price_component_load($price, 'base_price');
//  $tax = commerce_price_component_load($price, 'tax|vat');
  $price = $order_wrapper->commerce_order_total->value();
  $base_price = commerce_price_component_load($price, 'base_price');
  $shipping = commerce_price_component_load($price, 'shipping');
  // Get VAT:
  foreach(array('vat_deluxe', 'vat_food', 'vat_reduced') as $vat_type){
    $vat = commerce_price_component_load($price, 'tax|'.$vat_type);

    // Only one kind of VAT is used:
    if($vat) break;
  }

//  $base_price = $base_price[0]['price'];
  $shipping = $shipping[0]['price'];
  $vat = $vat[0]['price'];

  // VAT calculation:
  $rows = array();
  $row = array();

  $total_without_vat = 0;
  $total_vat = 0;
  $total = 0;
  // First row: product
  $tax_rate = commerce_tax_rate_load($vat['data']['tax_rate']['name']);
  $tax_rate = $tax_rate['rate']*100;
  $row[] = $tax_rate.'%';
  $total_without_vat += $price['amount'] - $vat['amount'];
  $total_vat += $vat['amount'];
  $total += $price['amount'] - $shipping['amount'];
  $row[] = commerce_currency_format($price['amount'] - $vat['amount'] - $shipping['amount'], $price['currency_code']);
  $row[] = commerce_currency_format($vat['amount'], $vat['currency_code']);
  $row[] = commerce_currency_format($price['amount'] - $shipping['amount'], $price['currency_code']);

  $rows[] = $row;

  $row = array();

  // Second row: shipping: Always Deluxe VAT:
  $tax_rate = commerce_tax_rate_load('vat_deluxe');
  $tax_rate = $tax_rate['rate']*100;
  $row[] = $tax_rate.'%';

  // The price for shipping has the VAT included, so:
  // base_price = 100*total/(100 + VAT)
  $shipping_base = 100*$shipping['amount']/(100 + $tax_rate);
  $total_without_vat += $shipping_base;
  $total_vat += $shipping['amount'] - $shipping_base;
  $total += $shipping['amount'];
  $row[] = commerce_currency_format($shipping_base, $shipping['currency_code']);
  $row[] = commerce_currency_format($shipping['amount'] - $shipping_base, $shipping['currency_code']);
  $row[] = commerce_currency_format($shipping['amount'], $shipping['currency_code']);

  $rows[] = $row;

  $row = array();
  //TOTAL:
  $row[] = t('Total');
  $row[] = commerce_currency_format($total_without_vat, $price['currency_code']);
  $row[] = commerce_currency_format($total_vat, $price['currency_code']);
  $row[] = commerce_currency_format($total, $price['currency_code']);

  $rows[] = $row;

  $tax_breakdown = array(
    '#theme' => 'table',
    '#empty' => t('There is not any line'),
    '#header' => $header,
    '#rows' => $rows,
  );

  $replacements['[order:summary]'] .= drupal_render($tax_breakdown);