--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snap_training.xml	Fri Oct 20 03:51:58 2017 -0400
@@ -0,0 +1,39 @@
+<?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>