#if $batch_key
  ln -s '${input_obj_file}' input.h5 &&
  PYTHONIOENCODING=utf-8 scanpy-cli integrate harmony
  --batch-key '${batch_key}'
  #if $basis
    --basis '${basis}'
  #end if
  --adjusted-basis '${adjusted_basis}'
  #if not $settings.default
      #if $settings.theta
      --theta '${settings.theta}'
      #end if 
      #if $settings.lambda
      --lambda '${settings.lambda}'
      #end if 
      #if $settings.sigma
      --sigma '${settings.sigma}'
      #end if 
      #if $settings.nclust
      --nclust '${settings.nclust}'
      #end if 
      #if $settings.tau
      --tau '${settings.tau}'
      #end if 
      #if $settings.block_size
      --block-size '${settings.block_size}'
      #end if 
      #if $settings.max_iter_cluster
      --max-iter-cluster '${settings.max_iter_cluster}'
      #end if 
      #if $settings.max_iter_harmony
      --max-iter-harmony '${settings.max_iter_harmony}'
      #end if 
      #if $settings.epsilon_cluster
      --epsilon-cluster '${settings.epsilon_cluster}'
      #end if 
      #if $settings.epsilon_harmony
      --epsilon-harmony '${settings.epsilon_harmony}'
      #end if 
      #if $settings.random_state
      --random-state '${settings.random_state}'
      #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