diff --git a/tools/chewbbaca/AlleleCall.xml b/tools/chewbbaca/AlleleCall.xml
index 971c4016c79..5507a9ae315 100644
--- a/tools/chewbbaca/AlleleCall.xml
+++ b/tools/chewbbaca/AlleleCall.xml
@@ -5,10 +5,12 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
+        #import re
         mkdir 'input' &&
         mkdir 'schema' &&
         #for $file in $input_file
-        ln -sf '$file' 'input/${file.element_identifier}.fa' &&
+        #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($file.element_identifier))
+        ln -sf '$file' 'input/${escaped_element_identifier}.${file.ext}' &&
         #end for
         unzip '$input_schema' -d 'schema' &&
         chewBBACA.py AlleleCall