ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-neighbors
#if $settings.default == "false"
    #if $settings.n_neighbors_file
        #set f = open($settings.n_neighbors_file.__str__)
        #set n_neighbors = f.read().strip()
        #silent f.close
    #elif $settings.n_neighbors
        #set n_neighbors = $settings.n_neighbors.__str__.strip()
    #end if

    #if $n_neighbors
        --n-neighbors $n_neighbors
    #end if
    #if $settings.key_added
        #set key_added = $settings.key_added
        #if $n_neighbors
            #set key_added = $key_added.replace('N_NEIGHBORS', $n_neighbors.__str__)
        #end if
        --key-added '${key_added}'
    #end if

    --method '${settings.method}'
    --metric '${settings.metric}'
    --random-state '${settings.random_seed}'
    #if $settings.use_rep
        --use-rep '${settings.use_rep}'
    #end if
    #if $settings.n_pcs
        --n-pcs '${settings.n_pcs}'
    #end if
    ${settings.knn}
#end if
    
    --input-format '${input_format}' input.h5
  
    
#if str($output_format).startswith('anndata')
    --show-obj stdout --output-format anndata output.h5
#else
    --show-obj stdout --output-format loom output.h5
#end if