<?xml version="1.0"?>
<macros>
	<xml name="requirements">
		<requirements>
			<requirement type="package" version="3.7">python</requirement>
			<requirement type="package" version="1.77">biopython</requirement>
			<requirement type="package" version="1.1.3">cpt_gffparser</requirement>  
			<yield/>
		</requirements>
	</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>
        <xml name="input/fasta">
		<param label="Fasta file" name="sequences" type="data" format="fasta"/>
	</xml>

	<token name="@SEQUENCE@">
		"$sequences"
	</token>
	<xml name="input/fasta/protein">
		<param label="Protein fasta file" name="sequences" type="data" format="fasta"/>
	</xml>
</macros>