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it should be possible using the Dynamic Input tool. Create a query as you would do using the Input Data tool in "Input Data Source Template" including the "Where" statement. Modify SQL Statement provides the option to replace your template where clause by the specific list of Ids from your file. This list can be generated using the Summarize tool (concatenate entries).
Let me know if it works for you or if you need more detail.
The SQL is missing the template where clause. I tihkn, you should add something like "WHERE b.Id IN('999999')" to your SQL (if b.Id is the field the restriction should be applied on).
In the "Update SQL" section, click on EDIT. In the drop-down, you have to select your where condition, Text to Replace would be '999999' and the Replacement Field is the concatenated field you created before.
double checked it with my database, it seems, concatenation and adding quotes are not needed, as the complete column is used for an "IN" statement. I've modified the sample, hopefully it works now as expected.