#if $tximport.tximport_selector == 'tximport':
    #if $tximport.mapping_format.mapping_format_selector == 'gtf':
        ln -s '$tximport.mapping_format.gtf_file' mapping.gff &&
    #else:
        ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
    #end if
#end if

## This is needed for Pulsar to transfer the file
cat '$__tool_directory__/get_deseq_dataset.R' > /dev/null &&

#import json
#import os
Rscript '${__tool_directory__}/deseq2.R'
    --cores \${GALAXY_SLOTS:-1}
    -o '$deseq_out'
    #if 'pdf' in $output_options.output_selector:
        -p '$plots'
    #end if
    -A $output_options.alpha_ma
    #if 'normCounts' in $output_options.output_selector:
        -n '$counts_out'
    #end if
    #if 'sizefactors' in $output_options.output_selector:
        -F '$sizefactors_out'
    #end if
    #if 'normRLog' in $output_options.output_selector:
        -r '$rlog_out'
    #end if
    #if 'normVST' in $output_options.output_selector:
        -v '$vst_out'
    #end if
    #set $filename_to_element_identifiers = {}
    #set $temp_factor_names = list()
    #for $factor in $select_data.rep_factorName:
        #set $temp_factor = list()
        #for $level in $factor.rep_factorLevel:
            #set $count_files = list()
            #if $select_data.how == 'group_tags':
                #for $group in $level.groups.value:
                    #for $file in $select_data.countsFile.get_datasets_for_group($group):
                        $count_files.append(str($file))
                        $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)),  $file.element_identifier)
                    #end for
                #end for
            #else:
                #for $file in $level.countsFile:
                    $count_files.append(str($file))
                    $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)),  $file.element_identifier)
                #end for
            #end if
            $temp_factor.append( {str($level.factorLevel): $count_files} )
        #end for
        $temp_factor.reverse()
        $temp_factor_names.append([str($factor.factorName), $temp_factor])
    #end for

    $header

    -f '#echo json.dumps(temp_factor_names)#'
    -l '#echo json.dumps(filename_to_element_identifiers)#'
    #if $advanced_options.esf_cond.esf:
        #if $advanced_options.esf_cond.esf == "user":
            -e $advanced_options.esf_cond.size_factor_input
        #else:
            -e $advanced_options.esf_cond.esf
        #end if
    #end if
    -t $advanced_options.fit_type
    #if $batch_factors:
        --batch_factors '$batch_factors'
    #end if
    #if $advanced_options.prefilter_conditional.prefilter:
        $advanced_options.prefilter_conditional.prefilter
        -V $advanced_options.prefilter_conditional.prefilter_value
    #end if
    
    $advanced_options.outlier_replace_off
    $advanced_options.outlier_filter_off
    $advanced_options.auto_mean_filter_off
    $advanced_options.use_beta_priors

    #if 'many_contrasts' in $output_options.output_selector
        -m
    #end if
    #if $tximport.tximport_selector == 'tximport':
        -i
        -y $tximport.txtype
        #if $tximport.mapping_format.mapping_format_selector == 'gtf':
            -x mapping.gff
        #else:
            -x mapping.txt
        #end if
    #end if