Batch files should be able to have input files too

Author: bethac07

worker/cp-worker.py

@@ -160,7 +160,7 @@ def runCellProfiler(message):
         cmd = cmdstem + '-p %(DATA)s/%(PL)s -i %(DATA)s/%(IN)s -o %(OUT)s -d ' + cpDone
         cmd += ' --data-file=%(DATA)s/%(FL)s -g %(Metadata)s'
     else:
-        cmd = cmdstem + '-p %(DATA)s/%(PL)s -o %(OUT)s -d ' + cpDone + ' --data-file=%(DATA)s/%(FL)s -g %(Metadata)s'
+        cmd = cmdstem + '-p %(DATA)s/%(PL)s -i %(DATA)s/%(IN)s -o %(OUT)s -d ' + cpDone + ' --data-file=%(DATA)s/%(FL)s -g %(Metadata)s'
     cmd = cmd % replaceValues
     print('Running', cmd)
     logger.info(cmd)