#set embeddings_tsv='embeddings.tsv'
ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-run-tsne
#if $use_rep
    --use-rep '${use_rep}'
#end if
#if $embeddings
    --export-embedding embeddings.tsv
#end if
#if $settings.default == "false"
    #if $settings.perplexity_file
        #set f = open($settings.perplexity_file.__str__)
        #set perplexity = f.read().strip()
        #silent f.close
    #elif $settings.perplexity
        #set perplexity = $settings.perplexity.__str__.strip()
    #end if      
    #if $perplexity
        --perplexity '$perplexity'
    #end if
    #if $settings.key_added
        #set key_added = $settings.key_added
        #if $perplexity
            #set key_added = $key_added.replace('PERPLEXITY', $perplexity.__str__)
        #end if
        --key-added '${key_added}'
        #set embeddings_tsv="embeddings_" + $key_added.__str__ + ".tsv"    
    #end if
    --early-exaggeration '${settings.early_exaggeration}'
    --learning-rate '${settings.learning_rate}'
    #if $settings.n_pc
        --n-pcs ${settings.n_pc}
    #end if
    #if not $settings.fast_tsne
        --no-fast-tsne
    #end if
    #if $settings.n_job
        --n-jobs ${settings.n_job}
    #end if
    #if $settings.random_seed is not None
        --random-state ${settings.random_seed}
    #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