Shopify does not support creating product options and attributes at the admin panel. Accordingly, the Shopify API can't handle creating this type of data either.
Your source shopping cart will be converted into a product with variants in your Shopify store, and this includes any products with custom options.
Because of the Shopify variant and option limits, this generation will be overlooked if there are more than 100 variants. On this occasion, you can contact us and we will customize the generation of these variants according to your needs.
UPDATE (for Shopify 2.0):
Since the release of the new Shopify 2.0, there will be some changes in the migration process to Shopify:
Attributes will be migrated to product metafields.
Product with custom options will still be converted to product with variants. One product can have up to 100 variants and 3 options.