if [ -d '${kraken_database.fields.path}/${kraken_database.fields.name}' ]; then export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}/${kraken_database.fields.name}'; else export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}'; fi &&

        kraken
            --threads \${GALAXY_SLOTS:-1}
            --db "\$KRAKEN_DEFAULT_DB"
            ${only_classified_output}

            #if str( $quick_operation.quick ) == "yes":
                --quick
                --min-hits ${quick_operation.min_hits}

            #end if

            #if $single_paired.single_paired_selector == 'yes'
                #if $forward_input.is_of_type( 'fastq' ):
                    --fastq-input
                #else:
                    --fasta-input
                #end if
                '${single_paired.forward_input}' '${single_paired.reverse_input}'
                ${single_paired.check_names}
            #elif $single_paired.single_paired_selector == "collection":
                #if $single_paired.input_pair.forward.is_of_type( 'fastq' ):
                    --fastq-input
                #else:
                    --fasta-input
                #end if
                '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
                ${single_paired.check_names}
            #else:
                #if $single_paired.input_sequences.is_of_type('fastq')
                    --fastq-input
                #else:
                    --fasta-input
                #end if
                '${single_paired.input_sequences}'
            #end if

            #if $split_reads:
                --classified-out '${classified_out}' --unclassified-out '${unclassified_out}'
            #end if

            ## The --output option was changed to redirect as it does not work properly is some situations. For example, on test database the tool classifies 4 reads but does not write them into a file if --output is specified. It does however print correct output into STDOUT. This behavior can be re-created with test database provided in test-data/test_db/ folder. This is the reason for incrementing version number from 1.1.2 to 1.1.3

            > '${output}'
            ##kraken-translate --db '${kraken_database.fields.name}' '${output}' > '${translated}'