cuffdiff
            --no-update-check
            --quiet
            --FDR=$fdr
            --num-threads="\${GALAXY_SLOTS:-4}"
            --min-alignment-count=$min_alignment_count
            --library-norm-method=$library_norm_method
            --dispersion-method=$dispersion_method

            ## Set advanced SE data parameters?
            #if $additional.sAdditional == "Yes":
                -m $additional.frag_mean_len
                -s $additional.frag_len_std_dev
            #end if

            ## Multi-read correct?
            #if $multiread_correct :
                -u
            #end if

            ## Bias correction?
            #if $bias_correction.do_bias_correction == "Yes":
               -b
                #if $bias_correction.seq_source.index_source == "history":
                    ## Custom genome from history.
                    '$bias_correction.seq_source.ref_file'
                #else:
                    ## Built-in genome.
                    '${bias_correction.seq_source.index.fields.path}'
                #end if
            #end if

            
#import re
#if $in_type.set_in_type in ['BAM', 'CXB']
    #set labels = "','".join([str($condition.name) for $condition in $in_type.conditions])
#elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST']
    #set labels = "','".join([str($condition).replace(',', '_') for $condition in $in_type.conditions.keys()])
#end if
--labels '$labels'
    

            $length_correction

            ## Set advanced parameters for cufflinks
             #if $advanced_settings.sAdvanced == "Yes":
                #if str($advanced_settings.library_type) != 'auto':
                        --library-type=$advanced_settings.library_type
                #end if
                #if $advanced_settings.mask_file:
                        --mask-file '$advanced_settings.mask_file'
                    #end if
                #if $advanced_settings.time_series:
                        --time-series
                #end if
                --max-mle-iterations=$advanced_settings.max_mle_iterations
                $advanced_settings.hits_norm
                --max-bundle-frags=$advanced_settings.max_bundle_frags
                --num-frag-count-draws=$advanced_settings.num_frag_count_draws
                --num-frag-assign-draws=$advanced_settings.num_frag_assign_draws
                --min-reps-for-js-test=$advanced_settings.min_reps_for_js_test
            #end if
            ## Inputs.
            '$gtf_input'

            
#if $in_type.set_in_type in ['BAM', 'CXB']
    #for $condition in $in_type.conditions:
        #set samples = ','.join([str($sample) for $sample in $condition.samples])
        '$samples'
    #end for
#elif $in_type.set_in_type == 'CONDITION_LIST'
    #for $sample in $in_type.conditions:
        '$sample'
    #end for
#elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST'
    #for $condition_list in $in_type.conditions:
        #set samples = ','.join([str($sample) for $sample in $condition_list])
        '$samples'
    #end for
#end if
    
            #if $generate_sqlite:
                &&
                Rscript '$__tool_directory__/cummeRbund.R'
            #end if