<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package">progressivemauve</requirement>
            <!--<requirement type="package" version="2.7">python</requirement>-->
            <requirement type="package" version="0.6.4">bcbiogff</requirement>
            <yield/>
        </requirements>
    </xml>
    <token name="@WRAPPER_VERSION@">2.4.0</token>
    <xml name="citation/progressive_mauve">
        <citation type="doi">10.1371/journal.pone.0011147</citation>
    </xml>
    <xml name="citation/gepard">
        <citation type="doi">10.1093/bioinformatics/btm039</citation>
    </xml>
    <token name="@XMFA_INPUT@">
		'$xmfa'
	</token>
    <xml name="xmfa_input" token_formats="xmfa">
        <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA"/>
    </xml>
    <token name="@XMFA_FA_INPUT@">
		'$sequences'
	</token>
    <xml name="xmfa_fa_input">
        <param type="data" format="fasta" name="sequences" label="Sequences in alignment" help="These sequences should be the SAME DATASET that was used in the progressiveMauve run. Failing that, they should be provided in the same order as in original progressiveMauve run"/>
    </xml>
    <xml name="genome_selector">
        <conditional name="reference_genome">
            <param name="reference_genome_source" type="select" label="Reference Genome">
                <option value="history" selected="True">From History</option>
                <option value="cached">Locally Cached</option>
            </param>
            <when value="cached">
                <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
                    <options from_data_table="all_fasta"/>
                </param>
            </when>
            <when value="history">
                <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
            </when>
        </conditional>
    </xml>
    <xml name="gff3_input">
        <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
    </xml>
    <xml name="input/gff3+fasta">
        <expand macro="gff3_input"/>
        <expand macro="genome_selector"/>
    </xml>
    <token name="@INPUT_GFF@">
	    '$gff3_data'
	</token>
    <token name="@INPUT_FASTA@">
    #if str($reference_genome.reference_genome_source) == 'cached':
            '${reference_genome.fasta_indexes.fields.path}'
    #else if str($reference_genome.reference_genome_source) == 'history':
            genomeref.fa
    #end if
	</token>
    <token name="@GENOME_SELECTOR_PRE@">
    #if $reference_genome.reference_genome_source == 'history':
            ln -s '$reference_genome.genome_fasta' genomeref.fa;
    #end if
	</token>
    <token name="@GENOME_SELECTOR@">
    #if str($reference_genome.reference_genome_source) == 'cached':
            '${reference_genome.fasta_indexes.fields.path}'
    #else if str($reference_genome.reference_genome_source) == 'history':
            genomeref.fa
    #end if
	</token>
</macros>