Is the ToolFactory a complete replacement for manual tool building?

• No, except where all the requirements for the package or script can be satisfied by the limited automated functions of the code generator, or where there is a script with all the complex logic that might otherwise go into XML
• Many advanced XML features are not available such as output filters.
• Adding DIY output filters, XML macros and some other advanced features is possible if anyone is sufficiently enthusiastic - some features in the galaxyxml package would be relatively straightforward to add.

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