#import os
#set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
#set input_with_ext = '.'.join([input_sans_ext, $input.ext])
ln -s '$input.file_name' '$input_with_ext' &&
#set output_log = 'output_log.txt'
touch '$output_log' &&
#if str($show) == 'Nothing':
    #set display_results = 'yes'
    #set all_results = 'yes'
    #set output_filename = ''
    #set output_datatype = ''
    #set results_filename = $results
#else:
    #set display_results = $display_results_cond.display_results
    #set all_results = $display_results_cond.all_results
    #set output_filename = '.'.join(['output', $input.ext])
    #set output_datatype = $input.ext
    touch '$output_filename' &&
    #if str($display_results_cond.display_results) == 'yes':
        #set results_filename = $results
    #else:
        #set results_filename = ''
    #end if
#end if
ImageJ --ij2 --headless --debug
--jython '$__tool_directory__/imagej2_analyze_particles_binary_jython_script.py'
'$output_log'
'$input'
'$black_background'
'$size'
$circularity_min
$circularity_max
'$show'
'$display_results'
'$all_results'
'$exclude_edges'
'$include_holes'
'$output_filename'
'$output_datatype'
'$results_filename'
&>'$output_log';
#if str($output_filename) != '':
    if [[ $? -ne 0 ]]; then
        cat '$output_log' >&2;
    else
        mv '$output_filename' '$output';
    fi
#else:
    if [[ $? -ne 0 ]]; then
        cat '$output_log' >&2;
    fi
#end if