From 959f4e7e590c33d8b646ffbb83e8c103dc0f6cb5 Mon Sep 17 00:00:00 2001
From: Dave B <dave@bx.psu.edu>
Date: Wed, 17 Jul 2019 11:23:47 -0400
Subject: [PATCH] Put dependency version and citation in a macro.

---
 tools/tn93/macros.xml     | 17 +++++++++++++++++
 tools/tn93/readreduce.xml | 18 ++++++------------
 tools/tn93/tn93.xml       | 20 ++++++++------------
 3 files changed, 31 insertions(+), 24 deletions(-)
 create mode 100644 tools/tn93/macros.xml

diff --git a/tools/tn93/macros.xml b/tools/tn93/macros.xml
new file mode 100644
index 00000000000..050c77a80a0
--- /dev/null
+++ b/tools/tn93/macros.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@VERSION@">1.0.4</token>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @UNPUBLISHED{spond,
+                    author = "Sergei Kosakovsky Pond",
+                    title = "HyPhy: Hypothesis Testing using Phylogenies",
+                    year = "2000",
+                    note = "http://hyphy.org/",
+                    url = "http://hyphy.org/"}
+            </citation>
+            <yield />
+        </citations>
+    </xml>
+</macros>
\ No newline at end of file
diff --git a/tools/tn93/readreduce.xml b/tools/tn93/readreduce.xml
index 92effcd846e..3da05d5b6f8 100644
--- a/tools/tn93/readreduce.xml
+++ b/tools/tn93/readreduce.xml
@@ -1,7 +1,10 @@
-<tool id="tn93_readreduce" name="Merge matching reads" version="1.0.4">
+<tool id="tn93_readreduce" name="Merge matching reads" version="@VERSION@">
     <description>into clusters with TN-93</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="1.0.4">tn93</requirement>
+        <requirement type="package" version="@VERSION@">tn93</requirement>
     </requirements>
     <version_command><![CDATA[tn93 --version]]></version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -62,14 +65,5 @@ readreduce
 Merge matching reads into clusters using the
 [Tamura Nei 93 distance](http://www.ncbi.nlm.nih.gov/pubmed/8336541) algorithm.
 ]]></help>
-    <citations>
-        <citation type="bibtex">
-            @UNPUBLISHED{spond,
-                author = "Sergei Kosakovsky Pond",
-                title = "HyPhy: Hypothesis Testing using Phylogenies",
-                year = "2000",
-                note = "http://hyphy.org/",
-                url = "http://hyphy.org/"}
-        </citation>
-    </citations>
+    <expand macro="citations" />
 </tool>
diff --git a/tools/tn93/tn93.xml b/tools/tn93/tn93.xml
index 6280c37f790..3fe93a854c0 100644
--- a/tools/tn93/tn93.xml
+++ b/tools/tn93/tn93.xml
@@ -1,7 +1,10 @@
-<tool id="tn93" name="TN93" version="1.0.4">
+<tool id="tn93" name="TN93" version="@VERSION@">
     <description>compute distances between aligned sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <requirements>
-        <requirement type="package" version="1.0.4">tn93</requirement>
+        <requirement type="package" version="@VERSION@">tn93</requirement>
     </requirements>
     <version_command><![CDATA[tn93 --version]]></version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -86,14 +89,7 @@ All sequences must be aligned and have the same length. Only IUPAC characters ar
 ':' can be replaced with another character using `-d`, and sequences that have no explicit copy number are assumed to be a single copy. Copy numbers
 only affect histogram and mean calculations.
 ]]></help>
-    <citations>
-        <citation type="bibtex">
-            @UNPUBLISHED{spond,
-                author = "Sergei Kosakovsky Pond",
-                title = "HyPhy: Hypothesis Testing using Phylogenies",
-                year = "2000",
-                note = "http://hyphy.org/",
-                url = "http://hyphy.org/"}
-        </citation>
-    </citations>
+    <expand macro="citations">
+        <citation type="doi">10.1093/oxfordjournals.molbev.a040023</citation>
+    </expand>
 </tool>