mkdir -p ~/.ncbi &&
        cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg &&
    
        
        #if $input.input_select == "sra_file":
            acc='${input.sra_file.name}' &&
            ln -s '${input.sra_file}' "\$acc" &&
        #else    
            #if $input.input_select == "file_list":
                #if $input.file_list.is_of_type('sra_manifest.tabular'):
                    #set $column = $input.file_list.unsanitized.metadata.column_names.index('Run') + 1
                    cut -f $column '$input.file_list'| tail -n +2 > accessions &&
                #else
                    
        grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
     '$input.file_list' > accessions &&
                #end if
            #elif $input.input_select == "accession_number":
                echo '${input.accession}' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions &&
            #end if
            for acc in \$(cat ./accessions);
            do (
                echo "Downloading accession: \$acc..." &&
        #end if  
    

        ## Do not use prefetch if region is specified, to avoid downloading
        ## the complete sra file.

        #if $input.input_select == "sra_file":
            sam-dump --log-level fatal  --accession '\$acc'
        #else:
            #if ( str( $adv.region ) == "" ):
                prefetch -X 200000000 "\$acc" &&
            #end if
            sam-dump --log-level fatal --disable-multithreading
        #end if

        #if str( $adv.region ) != "":
            --aligned-region '$adv.region'
        #end if
        #if str( $adv.matepairDist ) != "":
            --matepair-distance '$adv.matepairDist'
        #end if
        #if str( $adv.minMapq ) != "":
            --min-mapq '$adv.minMapq'
        #end if
        --header
        #if str( $adv.alignments ) == "both":
            --unaligned
        #end if

        #if str( $adv.alignments ) == "unaligned":
            --unaligned-spots-only
        #end if
        #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ):
            --primary
        #end if
        "\$acc"

        #if str( $outputformat ) == "bam":
            | samtools view -Sb - 2> /dev/null > "\$acc.bam"
        #elif str( $outputformat ) == "sam":
            > "\$acc.sam"
        #end if
        
        #if $input.input_select != "sra_file":
            ); done;
        #end if
        echo "Done with all accessions."