<?xml version="1.0"?>
<tool id="snap_training" name="Train SNAP" profile="16.04" version="@VERSION@">
    <description>ab-initio gene predictor</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="2.31.9">maker</requirement>
    </expand>
    <command><![CDATA[
        cp '${maker_gff}' input.gff3 &&
        echo "\##FASTA" >> input.gff3 &&
        cat '${genome}' >> input.gff3 &&
        maker2zff input.gff3 &&
        fathom -categorize ${gene_num} genome.ann genome.dna &&
        fathom -export ${gene_num} -plus uni.ann uni.dna &&
        forge export.ann export.dna &&
        hmm-assembler.pl snap_training . > '${output}'
    ]]></command>
    <inputs>
        <param name="genome" type="data" format="fasta" label="Genome to annotate"/>
        <param name="maker_gff" type="data" format="gff" label="Maker annotation to use for training"/>
        <param name="gene_num" type="integer" value="1000" label="Number of gene model to use for training"/>
    </inputs>
    <outputs>
        <data format="snaphmm" name="output" label="${tool.name} on ${on_string}: SNAP trained model"/>
    </outputs>
    <tests>
        <test>
            <param name="genome" value="human.fa"/>
            <param name="maker_gff" value="annot.gff3"/>
            <output name="output" compare="sim_size" file="snap.hmm"/>
        </test>
    </tests>
    <help><![CDATA[
        This tool allows to train SNAP (an ab-initio gene predictor) based on a previous prediction made with Maker.
    ]]></help>
    <expand macro="citations"/>
</tool>