ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-normalise-data
    #if not $settings.default 
        #if not $settings.log_transform
            ${settings.log_transform}
        #end if
        #if $settings.scale_factor
            --normalize-to '${settings.scale_factor}'
        #end if
        #if $settings.key_added
            --key-added '${settings.key_added}'
        #end if
        #if $settings.exclude.exclude_highly_expressed
            --exclude-highly-expressed --max-fraction '${settings.exclude.max_fraction}'
        #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
  
    
    #if $save_raw
      --save-raw
    #end if
    #if $save_layer
      --save-layer ${save_layer}
    #end if
  
    ${export_mtx}