--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hyphy_annotate.xml	Tue Apr 20 10:29:30 2021 +0000
@@ -0,0 +1,50 @@
+<?xml version="1.0"?>
+<tool id="hyphy_annotate" name="Annotate" version="@VERSION@">
+    <description>a newick tree with HyPhy</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        cp '$input_tree' input.nhx &&
+        cp '$compressed_msa' input.$compressed_msa.extension &&
+        cp '$__tool_directory__/scripts/annotator.bf' annotator.bf &&
+        hyphy annotator.bf
+            input.nhx '$root' input.$compressed_msa.extension '$label' labeled_tree.
+        @ERRORS@
+        ]]></command>
+    <inputs>
+        <param name="input_tree" type="data" format="nhx" label="Input tree" />
+        <param name="compressed_msa" type="data" format="fasta,fasta.gz" label="Multiple alignments" />
+        <param name="root" type="text" optional="false" value="REFERENCE" label="Root node" />
+        <param name="label" type="text" optional="false" value="Tree" label="Label for tree" />
+    </inputs>
+    <outputs>
+        <data name="labeled_tree_int" format="nhx" from_work_dir="labeled_tree.int.nwk" label="Labeled tree (int)" />
+        <data name="labeled_tree_clade" format="nhx" from_work_dir="labeled_tree.clade.nwk" label="Labeled tree (clade)" />
+        <data name="labeled_tree_full" format="nhx" from_work_dir="labeled_tree.full.nwk" label="Labeled tree (full)" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="compressed_msa" ftype="fasta.gz" value="annotate-in1.fa.gz"/>
+            <param name="input_tree" ftype="nhx" value="annotate-in1.nhx"/>
+            <param name="multiple_hits" value="None" />
+            <param name="root" value="REFERENCE" />
+            <param name="label" value="Annotated" />
+            <param name="log" value="false" />
+            <output name="labeled_tree_int" file="annotate-out1-int.nhx" />
+            <output name="labeled_tree_full" file="annotate-out1-full.nhx" />
+            <output name="labeled_tree_clade" file="annotate-out1-clade.nhx" />
+        </test>
+    </tests>
+    <help><![CDATA[
+HyPhy Annotate
+==============
+
+Given a set of alignments and a newick tree, this tool produces an annotated tree with
+the specified root node and label.
+]]></help>
+    <expand macro="citations">
+        <citation type="doi">10.1093/molbev/msv022</citation>
+    </expand>
+</tool>