#if $method_opts.method_opts_selector == "chemfp":
            ln -s '${method_opts.query_opts.targets}' ./targets.fps &&

            #if $method_opts.query_opts.query_opts_selector == "normal":
                ln -s '${method_opts.query_opts.query}' ./query.fps &&
            #end if

            simsearch
                #if int($method_opts.knn) == 0:
                    #set $k = 'all'
                    ## count is only available if k nearest neighbor search is disabled
                    $method_opts.counts
                #else:
                    #set $k = int($method_opts.knn)
                #end if

                -k $k
                --threshold $method_opts.threshold
                -o ./output.fps

                ## build and search an in-memory data structure (faster for multiple queries)
                --memory

                #if $method_opts.query_opts.query_opts_selector == "normal":
                    -q ./query.fps
                #else:
                    --NxN
                #end if

                ./targets.fps
                &&
                mv ./output.fps '${outfile}'
        #else:
            ## OpenBabel needs the original molecule file (molecule.'fileformat') next to the fastsearch index (molecule.fs). We use a composite datatype to accomplish that.
            ## Furthermore OpenBabel is really picky with file extensions. We need to specify every datatype. I did not find a solution to specify the query-filetype.
            ## A workaround is to create a symlink with a proper file-extension.
            ln -s '$method_opts.query' ./temp_query.$method_opts.query.ext
            obabel 
                -i fs '$method_opts.fastsearch.files_path/molecule.fs'
                -S ./temp_query.$method_opts.query.ext
                -at${method_opts.threshold}
                -O '${outfile}'
                -osmi
                -aa
        #end if