<?xml version="1.0"?>
<tool id="augustus_training" name="Train Augustus" profile="16.04" version="@VERSION@+galaxy1">
    <description>ab-initio gene predictor</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="2.31.10">maker</requirement>
    </expand>
    <command><![CDATA[
        cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&

        export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&

        maker2zff '${maker_gff}' &&

        zff2gff3.pl genome.ann | perl -plne 's/\t(\S+)$/\t\.\t$1/' > genome.gff3 &&

        autoAugTrain.pl --genome=${genome} --species=local --trainingset=genome.gff3 -v &&

        cd 'augustus_dir/species/' && tar cvfz '${output_tar}' 'local'
    ]]></command>
    <inputs>
        <param name="genome" type="data" format="fasta" label="Genome to annotate"/>
        <param name="maker_gff" type="data" format="gff" label="Annotation to use for training"/>
    </inputs>
    <outputs>
        <data name="output_tar" format="augustus" label="${tool.name} on ${on_string}: Augustus trained model"/>
    </outputs>
    <tests>
        <test expect_failure="true">
            <param name="genome" value="human_augustus.fa"/>
            <param name="maker_gff" value="annot.gff3"/>
            <assert_stderr>
                <has_text text="Number of training genes is with 2 too low (at least 100 genes required)" />
            </assert_stderr>
        </test>
    </tests>
    <help><![CDATA[
        This tool allows to train Augustus (the ab-initio gene predictor) based on a previous prediction (e.g. made with Maker).
    ]]></help>
    <expand macro="citations"/>
</tool>