ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-find-markers
#if $output_markers
    --save diffexp.tsv
#end if
    --n-genes '${n_genes}'
#if $groupby_file
    #set f = open($groupby_file.__str__)
    #set groupby = f.read().strip()
    #silent f.close
#else
    #set groupby = $groupby.replace('INPUT_OBJ', $input_obj_file.__getattr__('name'))
#end if
    --groupby '${groupby}'
#if $settings.default == "false"
    #if $settings.key_added
        #set key_added = $settings.key_added.replace('GROUPBY', $groupby.__str__)
        --key-added '${key_added}'
    #end if
    --method '${settings.method}'
    ${settings.rankby_abs}
    #if $settings.groups
        --groups '${settings.groups}'
    #end if
    --reference '${settings.reference}'
    #if $settings.filter.default == "false"
      --filter-params 'min_in_group_fraction:${settings.filter.min_in_group_fraction},max_out_group_fraction:${settings.filter.max_out_group_fraction},min_fold_change:${settings.filter.min_fold_change}'
    #end if
    #if $settings.layer
        --layer '${settings.layer}'
        --no-raw
    #else
        ${settings.use_raw}
    #end if
    $settings.pts $settings.tie_correct
    #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