ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-filter-cells
#if $gene_name
    --gene-name '${gene_name}'
#end if
#if $parameters
#for $p in $parameters
    #set $min = $p.min
    #set $max = $p.max
    #if $p.name.startswith('pct_')
      #set $min = float($min) / 100
      #set $max = float($max) / 100
    #end if
    --param 'c:$p.name' $min $max
#end for
#end if
#if $categories
    #set cats = ' '.join(["--category 'c:{name}' '{negate}{values}'".format(**$c) for $c in $categories])
    ${cats}
#end if
#if $subsets
    #set subs = ' '.join(["--subset 'c:{name}' '{subset}'".format(**$s) for $s in $subsets])
    ${subs}
#end if
    
    #if $save_raw
      --save-raw
    #end if
    #if $save_layer
      --save-layer ${save_layer}
    #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
  
    ${export_mtx}