Functoids are used in maps,So you can apply it to a XML node(field) in the map. You cannot directly apply it to the complete file.It will be individual node based. So if you have 10 fields(10 scripting functoid with C# code to remove the special characters) each connected to its own functoid and output to the corresponding field in the Output Schema. If the structure of the Output file is same as input file without special caracters then the Input and Output Schemas in the map will be same as of the incoming file.
If the Input file is not wellformed means it will not match the corresponding Schema and it will fail.
In that case you will need to create another Orchestration subscribing to the failed message and try to fix it using a .Net Helper Class method and reading each line as text and remove the special characters.
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