--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hyphy_gard.xml	Wed Aug 21 12:23:44 2019 -0400
@@ -0,0 +1,72 @@
+<?xml version="1.0"?>
+<tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy0">
+    <description>Genetic Algorithm for Recombination Detection</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input_file' gard_input.fa &&
+        @HYPHY_INVOCATION@ gard
+            --alignment ./gard_input.fa
+            --type '$datatype.value'
+            #if str($datatype.value) == 'Codon':
+                --code '$datatype.gencodeid'
+            #elif str($datatype.value) == 'Protein':
+                --model '$datatype.model'
+            #end if
+            --rv '$rate_cond.rate'
+            #if str($rate_cond.rate) != 'None':
+                --rate-classes '$rate_classes'
+            #end if
+            > '$gard_log'
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
+        <conditional name="datatype">
+            <param name="value" type="select" label="Type of data">
+                <option value="Nucleotide">Nucleotide</option>
+                <option value="Protein">Amino acid</option>
+                <option value="Codon">Codon</option>
+            </param>
+            <when value="Nucleotide"/>
+            <when value="Protein">
+                <expand macro="substitution" />
+            </when>
+            <when value="Codon">
+                <expand macro="gencode" />
+            </when>
+        </conditional>
+        <conditional name="rate_cond">
+            <param name="rate" type="select" label="Rate variation">
+                <option value="None">None</option>
+                <option value="GDD">General Discrete</option>
+                <option value="Gamma">Beta-Gamma</option>
+            </param>
+            <when value="None"/>
+            <when value="GDD">
+                <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/>
+            </when>
+            <when value="Gamma">
+                <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="gard_log" format="txt"/>
+        <data name="gard_output" format="nex" from_work_dir="gard_input.GARD_finalout"/>
+        <data name="translated" format="hyphy_results.json" from_work_dir="gard_input.fa.json"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="fasta" value="gard-in1.fa"/>
+            <output name="gard_output" file="gard-out1.nex" compare="sim_size" delta="160000"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+GARD (Genetic Algorithm for Recombination Detection) is a method to screen a multiple sequence analysis for the presence of recombination and is extremely useful as a pre-processing step for selection inference. Because recombinant sequences cannot be adequately described with a single phylogenetic history, selection inference on recombinant data often leads to a significant increase in false positives. GARD alleviates this concern by comprehensively screening an alignment for recombination breakpoints and inferring a unique phylogenetic history for each detected recombination block.
+    ]]></help>
+    <expand macro="citations">
+        <citation type="doi">10.1093/molbev/msl051</citation>
+    </expand>
+</tool>