[KaktoR]

First you have to call WemTool.exe with -e option from cmd or batch file to encode WEM files.

WemTool.exe -e

Then you can either call WemTool.exe with a batch file from inno setup or directly from the inno setup script within installation.

Example:
ISDone_Example.iss

if CurStep = ssPostInstall then
  begin
    ExtractTemporaryFile('WemTool.exe');
    FileCopy(ExpandConstant('{tmp}\WemTool.exe'), ExpandConstant('{app}\WemTool.exe'), False);
    ShellExec('open', ExpandConstant('{app}\WemTool.exe'), '-d', ExpandConstant('{app}'), SW_HIDE, ewWaitUntilTerminated, ResultCode);

DSG_Module.iss

[Files]
Source: "Include\WemTool.exe"; Flags: dontcopy

The above example will execute WemTool.exe with -d parameter after install process.

Example with batch execution:
ISDone_Example.iss

if (CurStep = ssPostInstall) then
  begin
    ExtractTemporaryFile('batch.bat');
    FileCopy(ExpandConstant('{tmp}\batch.bat'), ExpandConstant('{app}\batch,bat'), False);
    ShellExec('open', ExpandConstant('{app}\batch.bat'), '', '', SW_SHOWMINIMIZED, ewWaitUntilTerminated, ResultCode);

DSG_Module.iss

[Files]
Source: "Include\batch.bat"; Flags: dontcopy

Batch.bat

WemTool.exe -d

If you decide to use WemTool with batch file, you will see the actual progress of it.