The ability to use "input" function as an argument in "evalc" for execution is not available in MATLAB. Publishing a MATLAB-file involves evaluating the MATLAB file from the MATLAB command prompt, which is carried by the "evalc" command. When you are using "evalc", the functions "diary", "more" and "input" are disabled.
A workaround is to use input dialog boxes to get some control over the script's execution.