view macros.xml @ 3:fd70980a516b draft

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2019.06.05">regex</requirement>
            <requirement type="package" version="3.6">python</requirement>
            <requirement type="package" version="1.77">biopython</requirement>
            <requirement type="package" version="1.1.7">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>