export _JAVA_OPTIONS=-Duser.home=$__new_file_path__ &&
        python '$__tool_directory__/sirius_csifingerid.py'
            --input_pth '$input'
            --database $database
            --profile $profile
            --candidates $candidates
            --ppm_max $ppm_max
            --polarity $polarity
            --out_dir $__new_file_path__
            --canopus_result_pth canopus_all_summary.tsv
            --annotations_result_pth annotations_all_summary.tsv
            --all_structures_result_pth structures_all_summary.tsv
            --cores_top_level 1
            --cores_sirius \${GALAXY_SLOTS:-4}
            --meta_select_col $meta_select_col
            --min_MSMS_peaks $min_MSMS_peaks
            --schema $schema
            --temp_dir $__new_file_path__

            #if $adducts_cond.adducts_selector == 'select':
                #for $a in $adducts_cond.adducts
                    --adducts $a
                #end for
            #elif $adducts_cond.adducts_selector == 'all':
                #if $polarity == 'positive':
                    --adducts [M+H]+
                    --adducts [M+NH4]+
                    --adducts [M+Na]+
                    --adducts [M+K]+
                    --adducts [M+CH3OH+H]+
                    --adducts [M+ACN+H]+
                    --adducts [M+ACN+Na]+
                    --adducts [M+2ACN+H]+
                 #elif $polarity == 'negative':
                    --adducts [M-H]-
                    --adducts [M+Cl]-
                    --adducts [M+HCOO]-
                    --adducts [M+CH3COO]-
                 #end if
            #end if