#if $batch_key
  ln -s '${input_obj_file}' input.h5 &&
  PYTHONIOENCODING=utf-8 scanpy-integrate mnn 
  --batch-key '${batch_key}'
  #if $batch_layer
    --batch-layer '${batch_layer}'
  #end if
  #if $key_added
    --key-added '${key_added}'
  #end if
  #if $var_subset
    #set var_subsets = ' '.join(["--var-subset '{name}' '{values}'".format(**$v) for $v in $var_subset])
    ${var_subsets}
  #if $settings.default == "false"
    #if $settings.n_neighbors
        --n-neighbors '${settings.n_neighbors}'
    #end if
    #if $settings.sigma
        --sigma '${settings.sigma}'
    #end if
    #if not $settings.cos_norm_in
        ${settings.cos_norm_in}
    #end if
    #if $settings.svd_dim
        --svd-dim '${settings.svd_dim}'
    #end if
    #if not $settings.var_adj
        ${settings.var_adj}
    #end if
    #if $settings.compute_angle
        ${settings.compute_angle}
    #end if
    #if $settings.svd_mode
        --svd-mode '${settings.svd_mode}'
    #end if
  #end if
  
    #if $save_raw
      --save-raw
    #end if
    #if $save_layer
      --save-layer ${save_layer}
    #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