#if $reference_genome.source == 'history':
        ln -s '$reference_genome.genome_fasta' genomeref.fa &&
    #end if

    gffread '$input'
    #if $input.ext.startswith("bed")
        --in-bed
    #end if
    #if $reference_genome.source == 'cached':
        -g '${reference_genome.fasta_indexes.fields.path}'
        #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '':
            #echo ' '.join(str($reference_genome.ref_filtering).split(','))
        #end if
    #elif $reference_genome.source == 'history':
        -g genomeref.fa
        #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '':
            #echo ' '.join(str($reference_genome.ref_filtering).split(','))
        #end if
    #end if
    #if $filtering and str($filtering) != '':
        #echo " "
        #echo ' '.join(str($filtering).split(','))
    #end if
    #if $maxintron and $maxintron > 0:
        -i $maxintron
    #end if
    #if $region.region_filter == 'filter':
        -r '$region.range' $region.discard_partial
    #end if
    #if $merging.merge_sel != 'none':
        $merging.merge_cmd
        #if $merging.merge_options:
            #echo ' '.join(str($merging.merge_options).split(','))
        #end if
    #end if
    #if $chr_replace:
        -m '$chr_replace'
    #end if

    $full_gff_attribute_preservation
    $decode_url
    $expose

    ##
    ## Although documented, does not appear to be used in the gffread code
    ## #if $seq_info:
    ##     -A -s "$seq_info"
    ## #end if
    ##
    ## outputs
    #if $reference_genome.source != 'none':
        #if $reference_genome.fa_outputs and str($reference_genome.fa_outputs) != '':
            #echo ' ' + ' '.join(str($reference_genome.fa_outputs).split(','))
        #end if
    #end if

    #if $gffs.gff_fmt != 'none':
        #if $gffs.gff_fmt != 'bed' and $gffs.tname:
            -t '$gffs.tname'
        #end if
        #if $gffs.gff_fmt == 'gff':
            #if $input.datatype.file_ext == 'gtf':
                $gffs.ensembl
            #end if
        #end if
        #if $gffs.gff_fmt == 'gtf'
            -T
        #elif $gffs.gff_fmt == 'bed'
            --bed
        #end if
        -o output.$gffs.gff_fmt
    #else if 'fa_outputs' not in $reference_genome or '.fa' not in str($reference_genome['fa_outputs'])
        -o output.gff
    #end if

## Missing options
##
## --ids
## --nids
## -l 
## --jmatch
## --nc
## --ignore-locus
## -A -s (see above)
##  --sort-alpha : chromosomes (reference sequences) are sorted alphabetically
##  --sort-by : sort the reference sequences by the order in which their
##       names are given in the <refseq.lst> file
## Misc      
## --keep-exon-attrs : for -F option, do not attempt to reduce redundant
## --attrs
##      --keep-genes : in transcript-only mode (default), also preserve gene records
##      --keep-comments: for GFF3 input/output, try to preserve comments
## -B (see above)
## -P
##      --add-hasCDS : add a "hasCDS" attribute with value "true" for transcripts
##           that have CDS features
##      --adj-stop stop codon adjustment: enables -P and performs automatic
##           adjustment of the CDS stop coordinate if premature or downstream

##  --in-tlf: input GFF-like one-line-per-transcript format without exon/CDS
##            features (see --tlf option below); automatic if the input
##            filename ends with .tlf)
##  --stream: fast processing of input GFF/BED transcripts as they are received
##            ((no sorting, exons must be grouped by transcript in the input data)

## Clustering

## -Y

## Output 

## --gene2exon
## --t-adopt
## -j
## --w-add
## --w-nocds