--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hyphy_bgm.xml	Wed Aug 21 12:23:09 2019 -0400
@@ -0,0 +1,70 @@
+<?xml version="1.0"?>
+<tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy0">
+    <description>- Detecting coevolving sites via Bayesian graphical models</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input_file' bgm_input.fa &&
+        ln -s '$input_nhx' bgm_input.nhx &&
+        @HYPHY_INVOCATION@ bgm
+            --alignment ./bgm_input.fa
+            --tree ./bgm_input.nhx
+            --run_type $datatype.value
+            #if $datatype.value == "codon":
+                --code '$datatype.gencodeid'
+            #end if
+            #if $datatype.value == "protein":
+                --baseline_model '$datatype.model'
+            #end if
+            --branches '$branches'
+            --chain '$chain_length'
+            --burn_in '$burn_in'
+            --samples '$samples'
+            --parents '$parents'
+            --min_subs '$min_subs'
+            > '$bgm_log'
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
+        <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
+        <conditional name="datatype">
+            <param name="value" type="select" label="Type of data">
+                <option value="nucleotide">Nucleotide</option>
+                <option value="amino-acid">Amino acid</option>
+                <option value="codon">Codon</option>
+            </param>
+            <when value="nucleotide"/>
+            <when value="amino-acid">
+                <expand macro="substitution" />
+            </when>
+            <when value="codon">
+                <expand macro="gencode" />
+            </when>
+        </conditional>
+        <expand macro="branches"/>
+        <param name="chain_length" type="integer" value="100000" min="0" max="1000000000" label="Length of MCMC chain"/>
+        <param name="burn_in" type="integer" value="10000" min="0" max="1000000000" label="Number of samples to discard for burn-in"/>
+        <param name="samples" type="integer" value="100" min="0" max="100" label="Number of steps to extract from chain sample"/>
+        <param name="parents" type="integer" value="1" min="1" max="3" label="Maximum number of parents allowed per node"/>
+        <param name="min_subs" type="integer" value="1" min="1" max="100000" label="Minimum number of ubstitutions per site to be included in the analysis"/>
+    </inputs>
+    <outputs>
+        <data name="bgm_log" format="txt"/>
+        <data name="bgm_output" format="hyphy_results.json" from_work_dir="bgm_input.fa.BGM.json"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="fasta" value="bgm-in1.fa"/>
+            <param name="input_nhx" ftype="nhx" value="bgm-in1.nhx"/>
+            <output name="bgm_output" file="bgm-out1.json" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+The Bayesian Graphical Model (BGM) method is a tool for detecting coevolutionary interactions between amino acid positions in a protein.
+    ]]></help>
+    <expand macro="citations">
+        <citation type="doi">10.1371/journal.pcbi.0030231</citation>
+    </expand>
+</tool>