<?xml version="1.0"?>
<macros>
	<xml name="requirements">
		<requirements>
			<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>
	<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>
        <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>