I don't know ICS / IICS good enough to tell for sure, but in PowerCenter (the technical basis for ICS) you can edit the flat-file target definition and enter a "Format" definition for a numeric field. This "Format" description names the thousands separator (in your case a comma ",") and the decimal delimiter (in your case a period "."). You just enter these two characters into the "Format" field.
In PowerCenter you can do this either in the flat-file target definition or in the target instance in a mapping.
Again, no idea whether these points apply to ICS / IICS as well, I only hope so.
We currently do not have an option to specify thousands separator in IICS, however we do have a feature request raised to get this addressed in our future releases. You can track the progress of this FR with tracking id ICS-9362 through Informatica network portal.
Thanks for the info, so my suggestion can't be used here.
Depending on whether you work with numbers with a "fixed" maximum range (e.g. 0 - 9,999,999,999.999) or whether you work with larger ranges, you can either use a Java Transformation (leveraging the NumberFormatter class) or an Expression transformation to "translate" a numeric value to a string containing thousands separator and fractional delimiter.
If you need help with this, let us know, then we can explain how to do it.