--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snap.xml	Fri May 10 08:50:55 2019 -0400
@@ -0,0 +1,61 @@
+<tool id="snap" name="SNAP" profile="16.04" version="@VERSION@">
+    <description>gene prediction</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+        snap
+            -gff
+            $lcmask
+            #if $strand == 'forward'
+                -plus
+            #else if $strand == 'backward'
+                -minus
+            #end if
+            -aa '${output_aa}'
+            -tx '${output_tx}'
+            '${model}'
+            '${input_genome}'
+        > '${output_gff}'
+]]>
+    </command>
+    <inputs>
+        <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/>
+
+        <param name="model" type="data" format="snaphmm" label="Prediction model" help="File created with 'Train SNAP' tool"/>
+
+        <param argument="-lcmask" type="boolean"
+            label="Treat lowercase as N"
+            truevalue="-lcmask" falsevalue="" checked="false" />
+
+        <param name="strand" type="select"
+            label="Predict genes on specific strands">
+            <option value="both">both</option>
+            <option value="forward">forward</option>
+            <option value="backward">backward</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="gff" name="output_gff" label="${tool.name} on ${on_string}: GFF"/>
+        <data format="fasta" name="output_aa" label="${tool.name} on ${on_string}: Protein sequence"/>
+        <data format="fasta" name="output_tx" label="${tool.name} on ${on_string}: Coding sequence"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_genome" value="human.fa" ftype="fasta" />
+            <param name="model" value="snap.hmm" />
+            <!-- FIXME ftype temporarily removed because the not yet existing snaphmm type breaks travis tests -->
+            <!--param name="model" value="snap.hmm" ftype="snaphmm" /-->
+            <output name="output_gff" file="snap_annot.gff" ftype="gff"/>
+            <output name="output_aa" file="annot_aa.fasta" ftype="fasta"/>
+            <output name="output_tx" file="annot_tx.fasta" ftype="fasta"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+    SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>