<?xml version="1.0"?>
<macros>
	<xml name="requirements">
		<requirements>
			<requirement type="package">progressivemauve</requirement>
			<requirement type="package" version="3.8.13">python</requirement>
			<requirement type="package" version="1.79">biopython</requirement>
			<requirement type="package" version="1.2.2">cpt_gffparser</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">
	    <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
	</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@">
		genomeref.fa
	</token>
	<token name="@GENOME_SELECTOR_PRE@">
		ln -s $genome_fasta genomeref.fa;
	</token>
	<token name="@GENOME_SELECTOR@">
		genomeref.fa
	</token>
</macros>