#if $batch_key
  ln -s '${input_obj_file}' input.h5 &&
  PYTHONIOENCODING=utf-8 scanpy-integrate bbknn 
  --batch-key '${batch_key}'
  #if $settings.default == "false"
    #if $settings.use_rep
      --use-rep '${settings.use_rep}'
    #end if
    #if $settings.key_added
      --key-added '${settings.key_added}'
    #end if
    #if $settings.n_pcs
      --n-pcs '${settings.n_pcs}'
    #end if
    #if not $settings.approx
        ${settings.approx}
    #end if
    #if $settings.metric
        --metric '${settings.metric}'
    #end if
    #if $settings.neighbors_within_batch
        --neighbors-within-batch '${settings.neighbors_within_batch}'
    #end if
    #if $settings.trim
        --trim '${settings.trim}'
    #end if
    #if $settings.n_trees
        --n-trees '${settings.n_trees}'
    #end if
    #if not $settings.use_faiss
        ${settings.use_faiss}
    #end if
    #if $settings.set_op_mix_ratio
        --set-op-mix-ratio '${settings.set_op_mix_ratio}'
    #end if
    #if $settings.local_connectivity
        --local-connectivity '${settings.local_connectivity}'
    #end if
  #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
  
#else
echo "No batch variables passed, simply passing original input as output unchanged." && cp '${input_obj_file}' output.h5
#end if