--- a/simsearch.xml	Wed Mar 27 15:28:31 2013 -0400
+++ b/simsearch.xml	Sun Mar 31 13:17:04 2013 -0400
@@ -7,7 +7,7 @@
     <command>
         #if $method_opts.method_opts_selector == "chemfp":
             ## TODO: remove all comment lines, in muti mode many comment lines will be appear, also in the middle of the result file, remove them
-            simsearch -k $method_opts.k --threshold $method_opts.threshold --in fps --target-format fps -q "${method_opts.query}" "${method_opts.targets}" -o "${outfile}"
+            simsearch -k $method_opts.k --threshold $method_opts.threshold --query-format fps --target-format fps -q "${method_opts.query}" "${method_opts.targets}" -o "${outfile}"
         #else:
             ## OpenBabel needs the original molecule file (molecule.'fileformat') next to the fastsearch index (molecule.fs). We use a composite datatype to accomplish that.
             ## Furthermore OpenBabel is really picky with fileextensions. We need to specify every datatype. I did not find a solution to specify the query-filetype.