annotate cpt_starts/macros.xml @ 3:e4c2da570be1 draft default tip

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<?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>
	<token name="@BLAST_TSV@">
		"$blast_tsv"
	</token>
	<xml name="blast_tsv">
		<param label="Blast Results" help="TSV/tabular (25 Column)"
			name="blast_tsv" type="data" format="tabular" />
	</xml>

	<token name="@BLAST_XML@">
		"$blast_xml"
	</token>
	<xml name="blast_xml">
		<param label="Blast Results" help="XML format"
			name="blast_xml" type="data" format="blastxml" />
	</xml>
	<xml name="gff3_with_fasta">
	<param label="Genome Sequences" name="fasta" type="data" format="fasta" />
	<param label="Genome Annotations" name="gff3" type="data" format="gff3" />
	</xml>
	<xml name="genome_selector">
	    <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
	</xml>
	<xml name="gff3_input">
		<param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
	</xml>
	<xml name="input/gff3+fasta">
		<expand macro="gff3_input" />
		<expand macro="genome_selector" />
	</xml>
	<token name="@INPUT_GFF@">
	"$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>