ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-run-umap
#set neighbors_key = $use_graph.replace('INPUT_OBJ', $input_obj_file.__getattr__('name'))
#set embeddings_tsv='embeddings.tsv'
--neighbors-key '${neighbors_key}'
#if $key_added
    #if $neighbors_key
        #set key_added = $key_added.replace('NEIGHBORS_KEY', $neighbors_key.__str__)
    #set embeddings_tsv="embeddings_" + $key_added.__str__ + ".tsv"    
#end if
    --key-added '${key_added}'
#end if
#if $embeddings
    --export-embedding embeddings.tsv
#end if
#if $settings.default == "false"
    --n-components ${settings.n_components}
    --min-dist ${settings.min_dist}
    --spread ${settings.spread}
    --alpha ${settings.alpha}
    --gamma ${settings.gamma}
    --negative-sample-rate ${settings.negative_sample_rate}
    --random-state ${settings.random_seed}
    #if $settings.init_pos
        --init-pos '${settings.init_pos}'
    #end if
    #if $settings.maxiter
        --maxiter ${settings.maxiter}
    #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 $embeddings
    #if $embeddings_tsv != 'embeddings.tsv'
        && mv '${embeddings_tsv}' embeddings.tsv
    #end if
#end if