Thanks to Grant Shields:

To make a .bat document that will run PEBL programs from MediaLab, include the following two lines at the top of the file:

rem **read in first line from ML text file and store in subj variable
set /p subj=<C:\MediaLab\CurrentSubjectInfo.txt

rem **split first line into two tokens; subj# is second token
for /f "tokens=1,2 delims= " %%a in ("%subj%") do set s1=%%a&set s2=%%b

The above lines will automatically put the participant ID number into the PEBL program that starts. Following those two lines, modify the following line as necessary:

"C:\FULLPATHTOPEBL\pebl.exe" C:\FULLPATHTOEXPERIMENT\bcst-64.pbl -v sub1 -s %s2% --fullscreen --display 1024x768

You'll need to change the location of file paths (the document with the .pbl extension and the pebl.exe program) to whatever file you're trying to run.

Once you have your .bat script, you'll create a .que file like normal. In the file type, select "Executable," and set the file name to your .bat script. Don't specify any other parameters on that line. After that, you're done! You can add things before or after the line of the .bat file in the .que file.