--- a/napq.xml	Fri Jan 30 14:32:06 2015 +0100
+++ b/napq.xml	Fri Jan 30 14:37:28 2015 +0100
@@ -84,7 +84,16 @@
 	</inputs>
 	<configfiles>
 		<configfile name="identificationsConfigFile">## start comment
-		apml
+		## iterate over the selected files and store their names in the config file
+		#for $i, $s in enumerate( $identificationFileList )
+			${s.identificationsFile}
+			## also print out the datatype in the next line, based on previously configured datatype
+			#if isinstance( $s.identificationsFile.datatype, $__app__.datatypes_registry.get_datatype_by_extension('apml').__class__):
+				apml
+			#else:
+        		mzid
+      		#end if
+		#end for
 		## end comment</configfile>
 	</configfiles>
 	<outputs>