--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/augustus_training.xml	Fri Oct 20 03:55:35 2017 -0400
@@ -0,0 +1,43 @@
+<?xml version="1.0"?>
+<tool id="augustus_training" name="Train Augustus" 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 -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>