--- a/openms_wrapper.py	Fri May 10 17:31:59 2013 -0400
+++ b/openms_wrapper.py	Wed Jun 19 13:15:44 2013 -0400
@@ -71,10 +71,10 @@
            required:
             _fail("Failed to find specific OpenMS option [%s] in node [%s]" % (key, node))
     else:
-        if not node:
+        if node is None:
             _fail("Failed to find specific OpenMS option [%s] in node [%s]" % (key, node))
         sub_node = node.find("./NODE[@name='%s']" % key)
-        if not sub_node:
+        if sub_node is None:
             _fail("Failed to find node for key %s" % key)
         _set_option(sub_node, key_parts[1:], value, required)
 
@@ -145,8 +145,16 @@
     return None
 
 
+def _mapped_outputs(output_directory, inputs):
+    inputs = inputs.split(",")
+    os.makedirs(output_directory)
+    outputs = [os.path.join(output_directory, os.path.basename(input)) for input in inputs]
+    return ",".join(outputs)
+
+
 VALUE_FUNCTIONS = {compile(r"\@WHICH\((.*)\)\@"): _which,
                    compile(r"\@PEPNOVO_MODELS_PATH\@"): _get_pepnovo_models_path,
+                   compile(r"\@MULTI_OUTPUT\(([^,]*),(.*)\)\@"): _mapped_outputs,
                   }