From 4f6d344e620523fec729709f44cabfa8f6e7cf55 Mon Sep 17 00:00:00 2001
From: Saim Momin <mominsaim12@gmail.com>
Date: Fri, 24 Oct 2025 21:03:35 +0200
Subject: [PATCH 1/3] Initiate Beast2 wrappers: Push TreeAnnotator tool

---
 tools/beast2/.shed.yml                      |  16 ++
 tools/beast2/macros.xml                     |  29 ++++
 tools/beast2/test-data/input.trees          |  11 ++
 tools/beast2/test-data/output.trees         |  20 +++
 tools/beast2/test-data/output_burnout.trees |  20 +++
 tools/beast2/test-data/output_hpd.trees     |  20 +++
 tools/beast2/test-data/output_limit.trees   |  20 +++
 tools/beast2/test-data/output_no_sa.trees   |  20 +++
 tools/beast2/test-data/output_target.trees  |  20 +++
 tools/beast2/test-data/target.trees         |   9 ++
 tools/beast2/treeannotator.xml              | 157 ++++++++++++++++++++
 11 files changed, 342 insertions(+)
 create mode 100644 tools/beast2/.shed.yml
 create mode 100644 tools/beast2/macros.xml
 create mode 100644 tools/beast2/test-data/input.trees
 create mode 100644 tools/beast2/test-data/output.trees
 create mode 100644 tools/beast2/test-data/output_burnout.trees
 create mode 100644 tools/beast2/test-data/output_hpd.trees
 create mode 100644 tools/beast2/test-data/output_limit.trees
 create mode 100644 tools/beast2/test-data/output_no_sa.trees
 create mode 100644 tools/beast2/test-data/output_target.trees
 create mode 100644 tools/beast2/test-data/target.trees
 create mode 100644 tools/beast2/treeannotator.xml

diff --git a/tools/beast2/.shed.yml b/tools/beast2/.shed.yml
new file mode 100644
index 00000000000..4e920264517
--- /dev/null
+++ b/tools/beast2/.shed.yml
@@ -0,0 +1,16 @@
+name: beast2
+owner: iuc
+categories:
+- Phylogenetics
+description: "BEAST 2: Bayesian Evolutionary Analysis Sampling Trees"
+long_description: BEAST 2 is a software platform for Bayesian evolutionary analysis of molecular sequences using MCMC. It is designed for phylogenetic inference, divergence time estimation, and testing evolutionary hypotheses based on genetic data.
+homepage_url: https://www.beast2.org/
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/beast2
+type: unrestricted
+suite:
+  name: "suite_beast2"
+  description: "A suite of tools for BEAST 2 in Galaxy"
+  type: repository_suite_definition
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for the BEAST 2 tool suite: {{ tool_name }}"
\ No newline at end of file
diff --git a/tools/beast2/macros.xml b/tools/beast2/macros.xml
new file mode 100644
index 00000000000..a078124e89c
--- /dev/null
+++ b/tools/beast2/macros.xml
@@ -0,0 +1,29 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.5.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">25.0</token>
+    <xrefs>
+      <xref type="bio.tools">beast2</xref>
+    </xrefs>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">beast2</requirement>
+        </requirements>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">beast2</xref>
+        </xrefs>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1371/journal.pcbi.1003537</citation>
+        </citations>
+    </xml>
+    <xml name="creator">
+        <creator>
+            <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12"/>
+           <organization name="Galaxy Europe"/>
+        </creator>
+    </xml>
+</macros>
\ No newline at end of file
diff --git a/tools/beast2/test-data/input.trees b/tools/beast2/test-data/input.trees
new file mode 100644
index 00000000000..1ea00680453
--- /dev/null
+++ b/tools/beast2/test-data/input.trees
@@ -0,0 +1,11 @@
+#NEXUS
+begin trees;
+    translate
+        1 taxonA,
+        2 taxonB,
+        3 taxonC,
+        4 taxonD;
+    tree STATE_0 = [&R] ((1:0.1,2:0.1):0.2,(3:0.15,4:0.15):0.25):0.1;
+    tree STATE_1 = [&R] ((1:0.12,2:0.12):0.18,(3:0.14,4:0.14):0.27):0.11;
+    tree STATE_2 = [&R] ((1:0.09,2:0.09):0.22,(3:0.16,4:0.16):0.24):0.09;
+end
\ No newline at end of file
diff --git a/tools/beast2/test-data/output.trees b/tools/beast2/test-data/output.trees
new file mode 100644
index 00000000000..08cd60ce9d2
--- /dev/null
+++ b/tools/beast2/test-data/output.trees
@@ -0,0 +1,20 @@
+#NEXUS
+
+Begin taxa;
+	Dimensions ntax=4;
+		Taxlabels
+			taxonA 
+			taxonB 
+			taxonC 
+			taxonD
+			;
+End;
+Begin trees;
+	Translate
+		   1 taxonA,
+		   2 taxonB,
+		   3 taxonC,
+		   4 taxonD
+;
+tree TREE1 = ((1[&CAheight_95%_HPD={0.08999999999999997,0.11000000000000004},CAheight_mean=0.09999999999999999,CAheight_median=0.09999999999999998,CAheight_range={0.08999999999999997,0.11000000000000004},height=0.09999999999999999,height_95%_HPD={0.08999999999999997,0.11000000000000004},height_median=0.09999999999999998,height_range={0.08999999999999997,0.11000000000000004},length=0.10333333333333333,length_95%_HPD={0.09000000000000002,0.12},length_median=0.09999999999999998,length_range={0.09000000000000002,0.12}]:0.10333333333333335,2[&CAheight_95%_HPD={0.08999999999999997,0.11000000000000004},CAheight_mean=0.09999999999999999,CAheight_median=0.09999999999999998,CAheight_range={0.08999999999999997,0.11000000000000004},height=0.09999999999999999,height_95%_HPD={0.08999999999999997,0.11000000000000004},height_median=0.09999999999999998,height_range={0.08999999999999997,0.11000000000000004},length=0.10333333333333333,length_95%_HPD={0.09000000000000002,0.12},length_median=0.09999999999999998,length_range={0.09000000000000002,0.12}]:0.10333333333333335)[&CAheight_95%_HPD={0.18,0.23000000000000004},CAheight_mean=0.20333333333333334,CAheight_median=0.19999999999999996,CAheight_range={0.18,0.23000000000000004},height=0.20333333333333334,height_95%_HPD={0.18,0.23000000000000004},height_median=0.19999999999999996,height_range={0.18,0.23000000000000004},length=0.20000000000000004,length_95%_HPD={0.18,0.22000000000000003},length_median=0.20000000000000007,length_range={0.18,0.22000000000000003},posterior=1.0]:0.19999999999999998,(3[&height=0.0,length=0.15000000000000002,length_95%_HPD={0.14,0.16000000000000003},length_median=0.15000000000000002,length_range={0.14,0.16000000000000003}]:0.15000000000000002,4[&height=0.0,length=0.15000000000000002,length_95%_HPD={0.14,0.16000000000000003},length_median=0.15000000000000002,length_range={0.14,0.16000000000000003}]:0.15000000000000002)[&CAheight_95%_HPD={0.14,0.16000000000000003},CAheight_mean=0.15000000000000002,CAheight_median=0.15000000000000002,CAheight_range={0.14,0.16000000000000003},height=0.15000000000000002,height_95%_HPD={0.14,0.16000000000000003},height_median=0.15000000000000002,height_range={0.14,0.16000000000000003},length=0.25333333333333335,length_95%_HPD={0.24,0.27},length_median=0.25,length_range={0.24,0.27},posterior=1.0]:0.2533333333333333)[&CAheight_95%_HPD={0.4,0.41000000000000003},CAheight_mean=0.4033333333333333,CAheight_median=0.4,CAheight_range={0.4,0.41000000000000003},height=0.4033333333333333,height_95%_HPD={0.4,0.41000000000000003},height_median=0.4,height_range={0.4,0.41000000000000003},length=0.0,posterior=1.0]:0.0;
+End;
diff --git a/tools/beast2/test-data/output_burnout.trees b/tools/beast2/test-data/output_burnout.trees
new file mode 100644
index 00000000000..2b40c57d106
--- /dev/null
+++ b/tools/beast2/test-data/output_burnout.trees
@@ -0,0 +1,20 @@
+#NEXUS
+
+Begin taxa;
+	Dimensions ntax=4;
+		Taxlabels
+			taxonA 
+			taxonB 
+			taxonC 
+			taxonD
+			;
+End;
+Begin trees;
+	Translate
+		   1 taxonA,
+		   2 taxonB,
+		   3 taxonC,
+		   4 taxonD
+;
+tree TREE1 = ((1[&height=0.09999999999999999,height_95%_HPD={0.08999999999999997,0.11000000000000004},height_median=0.09999999999999998,height_range={0.08999999999999997,0.11000000000000004},length=0.10333333333333333,length_95%_HPD={0.09000000000000002,0.12},length_median=0.09999999999999998,length_range={0.09000000000000002,0.12}]:0.09999999999999998,2[&height=0.09999999999999999,height_95%_HPD={0.08999999999999997,0.11000000000000004},height_median=0.09999999999999998,height_range={0.08999999999999997,0.11000000000000004},length=0.10333333333333333,length_95%_HPD={0.09000000000000002,0.12},length_median=0.09999999999999998,length_range={0.09000000000000002,0.12}]:0.09999999999999998)[&height=0.20333333333333334,height_95%_HPD={0.18,0.23000000000000004},height_median=0.19999999999999996,height_range={0.18,0.23000000000000004},length=0.20000000000000004,length_95%_HPD={0.18,0.22000000000000003},length_median=0.20000000000000007,length_range={0.18,0.22000000000000003},posterior=1.0]:0.20000000000000007,(3[&height=0.0,length=0.15000000000000002,length_95%_HPD={0.14,0.16000000000000003},length_median=0.15000000000000002,length_range={0.14,0.16000000000000003}]:0.15000000000000002,4[&height=0.0,length=0.15000000000000002,length_95%_HPD={0.14,0.16000000000000003},length_median=0.15000000000000002,length_range={0.14,0.16000000000000003}]:0.15000000000000002)[&height=0.15000000000000002,height_95%_HPD={0.14,0.16000000000000003},height_median=0.15000000000000002,height_range={0.14,0.16000000000000003},length=0.25333333333333335,length_95%_HPD={0.24,0.27},length_median=0.25,length_range={0.24,0.27},posterior=1.0]:0.25)[&height=0.4033333333333333,height_95%_HPD={0.4,0.41000000000000003},height_median=0.4,height_range={0.4,0.41000000000000003},length=0.0,posterior=1.0]:0.0;
+End;
diff --git a/tools/beast2/test-data/output_hpd.trees b/tools/beast2/test-data/output_hpd.trees
new file mode 100644
index 00000000000..08cd60ce9d2
--- /dev/null
+++ b/tools/beast2/test-data/output_hpd.trees
@@ -0,0 +1,20 @@
+#NEXUS
+
+Begin taxa;
+	Dimensions ntax=4;
+		Taxlabels
+			taxonA 
+			taxonB 
+			taxonC 
+			taxonD
+			;
+End;
+Begin trees;
+	Translate
+		   1 taxonA,
+		   2 taxonB,
+		   3 taxonC,
+		   4 taxonD
+;
+tree TREE1 = ((1[&CAheight_95%_HPD={0.08999999999999997,0.11000000000000004},CAheight_mean=0.09999999999999999,CAheight_median=0.09999999999999998,CAheight_range={0.08999999999999997,0.11000000000000004},height=0.09999999999999999,height_95%_HPD={0.08999999999999997,0.11000000000000004},height_median=0.09999999999999998,height_range={0.08999999999999997,0.11000000000000004},length=0.10333333333333333,length_95%_HPD={0.09000000000000002,0.12},length_median=0.09999999999999998,length_range={0.09000000000000002,0.12}]:0.10333333333333335,2[&CAheight_95%_HPD={0.08999999999999997,0.11000000000000004},CAheight_mean=0.09999999999999999,CAheight_median=0.09999999999999998,CAheight_range={0.08999999999999997,0.11000000000000004},height=0.09999999999999999,height_95%_HPD={0.08999999999999997,0.11000000000000004},height_median=0.09999999999999998,height_range={0.08999999999999997,0.11000000000000004},length=0.10333333333333333,length_95%_HPD={0.09000000000000002,0.12},length_median=0.09999999999999998,length_range={0.09000000000000002,0.12}]:0.10333333333333335)[&CAheight_95%_HPD={0.18,0.23000000000000004},CAheight_mean=0.20333333333333334,CAheight_median=0.19999999999999996,CAheight_range={0.18,0.23000000000000004},height=0.20333333333333334,height_95%_HPD={0.18,0.23000000000000004},height_median=0.19999999999999996,height_range={0.18,0.23000000000000004},length=0.20000000000000004,length_95%_HPD={0.18,0.22000000000000003},length_median=0.20000000000000007,length_range={0.18,0.22000000000000003},posterior=1.0]:0.19999999999999998,(3[&height=0.0,length=0.15000000000000002,length_95%_HPD={0.14,0.16000000000000003},length_median=0.15000000000000002,length_range={0.14,0.16000000000000003}]:0.15000000000000002,4[&height=0.0,length=0.15000000000000002,length_95%_HPD={0.14,0.16000000000000003},length_median=0.15000000000000002,length_range={0.14,0.16000000000000003}]:0.15000000000000002)[&CAheight_95%_HPD={0.14,0.16000000000000003},CAheight_mean=0.15000000000000002,CAheight_median=0.15000000000000002,CAheight_range={0.14,0.16000000000000003},height=0.15000000000000002,height_95%_HPD={0.14,0.16000000000000003},height_median=0.15000000000000002,height_range={0.14,0.16000000000000003},length=0.25333333333333335,length_95%_HPD={0.24,0.27},length_median=0.25,length_range={0.24,0.27},posterior=1.0]:0.2533333333333333)[&CAheight_95%_HPD={0.4,0.41000000000000003},CAheight_mean=0.4033333333333333,CAheight_median=0.4,CAheight_range={0.4,0.41000000000000003},height=0.4033333333333333,height_95%_HPD={0.4,0.41000000000000003},height_median=0.4,height_range={0.4,0.41000000000000003},length=0.0,posterior=1.0]:0.0;
+End;
diff --git a/tools/beast2/test-data/output_limit.trees b/tools/beast2/test-data/output_limit.trees
new file mode 100644
index 00000000000..653bfaf6db4
--- /dev/null
+++ b/tools/beast2/test-data/output_limit.trees
@@ -0,0 +1,20 @@
+#NEXUS
+
+Begin taxa;
+	Dimensions ntax=4;
+		Taxlabels
+			taxonA 
+			taxonB 
+			taxonC 
+			taxonD
+			;
+End;
+Begin trees;
+	Translate
+		   1 taxonA,
+		   2 taxonB,
+		   3 taxonC,
+		   4 taxonD
+;
+tree TREE1 = ((1[&height=0.09999999999999999,height_95%_HPD={0.08999999999999997,0.11000000000000004},height_median=0.09999999999999998,height_range={0.08999999999999997,0.11000000000000004},length=0.10333333333333333,length_95%_HPD={0.09000000000000002,0.12},length_median=0.09999999999999998,length_range={0.09000000000000002,0.12}]:0.10333333333333335,2[&height=0.09999999999999999,height_95%_HPD={0.08999999999999997,0.11000000000000004},height_median=0.09999999999999998,height_range={0.08999999999999997,0.11000000000000004},length=0.10333333333333333,length_95%_HPD={0.09000000000000002,0.12},length_median=0.09999999999999998,length_range={0.09000000000000002,0.12}]:0.10333333333333335)[&height=0.20333333333333334,height_95%_HPD={0.18,0.23000000000000004},height_median=0.19999999999999996,height_range={0.18,0.23000000000000004},length=0.20000000000000004,length_95%_HPD={0.18,0.22000000000000003},length_median=0.20000000000000007,length_range={0.18,0.22000000000000003},posterior=1.0]:0.19999999999999998,(3[&height=0.0,length=0.15000000000000002,length_95%_HPD={0.14,0.16000000000000003},length_median=0.15000000000000002,length_range={0.14,0.16000000000000003}]:0.15000000000000002,4[&height=0.0,length=0.15000000000000002,length_95%_HPD={0.14,0.16000000000000003},length_median=0.15000000000000002,length_range={0.14,0.16000000000000003}]:0.15000000000000002)[&height=0.15000000000000002,height_95%_HPD={0.14,0.16000000000000003},height_median=0.15000000000000002,height_range={0.14,0.16000000000000003},length=0.25333333333333335,length_95%_HPD={0.24,0.27},length_median=0.25,length_range={0.24,0.27},posterior=1.0]:0.2533333333333333)[&height=0.4033333333333333,height_95%_HPD={0.4,0.41000000000000003},height_median=0.4,height_range={0.4,0.41000000000000003},length=0.0,posterior=1.0]:0.0;
+End;
diff --git a/tools/beast2/test-data/output_no_sa.trees b/tools/beast2/test-data/output_no_sa.trees
new file mode 100644
index 00000000000..08cd60ce9d2
--- /dev/null
+++ b/tools/beast2/test-data/output_no_sa.trees
@@ -0,0 +1,20 @@
+#NEXUS
+
+Begin taxa;
+	Dimensions ntax=4;
+		Taxlabels
+			taxonA 
+			taxonB 
+			taxonC 
+			taxonD
+			;
+End;
+Begin trees;
+	Translate
+		   1 taxonA,
+		   2 taxonB,
+		   3 taxonC,
+		   4 taxonD
+;
+tree TREE1 = ((1[&CAheight_95%_HPD={0.08999999999999997,0.11000000000000004},CAheight_mean=0.09999999999999999,CAheight_median=0.09999999999999998,CAheight_range={0.08999999999999997,0.11000000000000004},height=0.09999999999999999,height_95%_HPD={0.08999999999999997,0.11000000000000004},height_median=0.09999999999999998,height_range={0.08999999999999997,0.11000000000000004},length=0.10333333333333333,length_95%_HPD={0.09000000000000002,0.12},length_median=0.09999999999999998,length_range={0.09000000000000002,0.12}]:0.10333333333333335,2[&CAheight_95%_HPD={0.08999999999999997,0.11000000000000004},CAheight_mean=0.09999999999999999,CAheight_median=0.09999999999999998,CAheight_range={0.08999999999999997,0.11000000000000004},height=0.09999999999999999,height_95%_HPD={0.08999999999999997,0.11000000000000004},height_median=0.09999999999999998,height_range={0.08999999999999997,0.11000000000000004},length=0.10333333333333333,length_95%_HPD={0.09000000000000002,0.12},length_median=0.09999999999999998,length_range={0.09000000000000002,0.12}]:0.10333333333333335)[&CAheight_95%_HPD={0.18,0.23000000000000004},CAheight_mean=0.20333333333333334,CAheight_median=0.19999999999999996,CAheight_range={0.18,0.23000000000000004},height=0.20333333333333334,height_95%_HPD={0.18,0.23000000000000004},height_median=0.19999999999999996,height_range={0.18,0.23000000000000004},length=0.20000000000000004,length_95%_HPD={0.18,0.22000000000000003},length_median=0.20000000000000007,length_range={0.18,0.22000000000000003},posterior=1.0]:0.19999999999999998,(3[&height=0.0,length=0.15000000000000002,length_95%_HPD={0.14,0.16000000000000003},length_median=0.15000000000000002,length_range={0.14,0.16000000000000003}]:0.15000000000000002,4[&height=0.0,length=0.15000000000000002,length_95%_HPD={0.14,0.16000000000000003},length_median=0.15000000000000002,length_range={0.14,0.16000000000000003}]:0.15000000000000002)[&CAheight_95%_HPD={0.14,0.16000000000000003},CAheight_mean=0.15000000000000002,CAheight_median=0.15000000000000002,CAheight_range={0.14,0.16000000000000003},height=0.15000000000000002,height_95%_HPD={0.14,0.16000000000000003},height_median=0.15000000000000002,height_range={0.14,0.16000000000000003},length=0.25333333333333335,length_95%_HPD={0.24,0.27},length_median=0.25,length_range={0.24,0.27},posterior=1.0]:0.2533333333333333)[&CAheight_95%_HPD={0.4,0.41000000000000003},CAheight_mean=0.4033333333333333,CAheight_median=0.4,CAheight_range={0.4,0.41000000000000003},height=0.4033333333333333,height_95%_HPD={0.4,0.41000000000000003},height_median=0.4,height_range={0.4,0.41000000000000003},length=0.0,posterior=1.0]:0.0;
+End;
diff --git a/tools/beast2/test-data/output_target.trees b/tools/beast2/test-data/output_target.trees
new file mode 100644
index 00000000000..08cd60ce9d2
--- /dev/null
+++ b/tools/beast2/test-data/output_target.trees
@@ -0,0 +1,20 @@
+#NEXUS
+
+Begin taxa;
+	Dimensions ntax=4;
+		Taxlabels
+			taxonA 
+			taxonB 
+			taxonC 
+			taxonD
+			;
+End;
+Begin trees;
+	Translate
+		   1 taxonA,
+		   2 taxonB,
+		   3 taxonC,
+		   4 taxonD
+;
+tree TREE1 = ((1[&CAheight_95%_HPD={0.08999999999999997,0.11000000000000004},CAheight_mean=0.09999999999999999,CAheight_median=0.09999999999999998,CAheight_range={0.08999999999999997,0.11000000000000004},height=0.09999999999999999,height_95%_HPD={0.08999999999999997,0.11000000000000004},height_median=0.09999999999999998,height_range={0.08999999999999997,0.11000000000000004},length=0.10333333333333333,length_95%_HPD={0.09000000000000002,0.12},length_median=0.09999999999999998,length_range={0.09000000000000002,0.12}]:0.10333333333333335,2[&CAheight_95%_HPD={0.08999999999999997,0.11000000000000004},CAheight_mean=0.09999999999999999,CAheight_median=0.09999999999999998,CAheight_range={0.08999999999999997,0.11000000000000004},height=0.09999999999999999,height_95%_HPD={0.08999999999999997,0.11000000000000004},height_median=0.09999999999999998,height_range={0.08999999999999997,0.11000000000000004},length=0.10333333333333333,length_95%_HPD={0.09000000000000002,0.12},length_median=0.09999999999999998,length_range={0.09000000000000002,0.12}]:0.10333333333333335)[&CAheight_95%_HPD={0.18,0.23000000000000004},CAheight_mean=0.20333333333333334,CAheight_median=0.19999999999999996,CAheight_range={0.18,0.23000000000000004},height=0.20333333333333334,height_95%_HPD={0.18,0.23000000000000004},height_median=0.19999999999999996,height_range={0.18,0.23000000000000004},length=0.20000000000000004,length_95%_HPD={0.18,0.22000000000000003},length_median=0.20000000000000007,length_range={0.18,0.22000000000000003},posterior=1.0]:0.19999999999999998,(3[&height=0.0,length=0.15000000000000002,length_95%_HPD={0.14,0.16000000000000003},length_median=0.15000000000000002,length_range={0.14,0.16000000000000003}]:0.15000000000000002,4[&height=0.0,length=0.15000000000000002,length_95%_HPD={0.14,0.16000000000000003},length_median=0.15000000000000002,length_range={0.14,0.16000000000000003}]:0.15000000000000002)[&CAheight_95%_HPD={0.14,0.16000000000000003},CAheight_mean=0.15000000000000002,CAheight_median=0.15000000000000002,CAheight_range={0.14,0.16000000000000003},height=0.15000000000000002,height_95%_HPD={0.14,0.16000000000000003},height_median=0.15000000000000002,height_range={0.14,0.16000000000000003},length=0.25333333333333335,length_95%_HPD={0.24,0.27},length_median=0.25,length_range={0.24,0.27},posterior=1.0]:0.2533333333333333)[&CAheight_95%_HPD={0.4,0.41000000000000003},CAheight_mean=0.4033333333333333,CAheight_median=0.4,CAheight_range={0.4,0.41000000000000003},height=0.4033333333333333,height_95%_HPD={0.4,0.41000000000000003},height_median=0.4,height_range={0.4,0.41000000000000003},length=0.0,posterior=1.0]:0.0;
+End;
diff --git a/tools/beast2/test-data/target.trees b/tools/beast2/test-data/target.trees
new file mode 100644
index 00000000000..b256ade77d5
--- /dev/null
+++ b/tools/beast2/test-data/target.trees
@@ -0,0 +1,9 @@
+#NEXUS
+begin trees;
+    translate
+        1 taxonA,
+        2 taxonB,
+        3 taxonC,
+        4 taxonD;
+    tree TARGET = [&R] ((1:0.1,2:0.1):0.2,(3:0.15,4:0.15):0.25):0.1;
+end;
diff --git a/tools/beast2/treeannotator.xml b/tools/beast2/treeannotator.xml
new file mode 100644
index 00000000000..f99340fe066
--- /dev/null
+++ b/tools/beast2/treeannotator.xml
@@ -0,0 +1,157 @@
+<tool id="beast2_treeannotator" name="TreeAnnotator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Summarize a sample of trees with annotations</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        treeannotator
+        -heights '$heights'
+        #if $burnin_source.burnin_selector == 'percentage':
+            -burnin $burnin_source.burnin_percent
+        #end if
+        #if $limit:
+            -limit $limit
+        #end if
+        #if $target:
+            -target '$target'
+        #end if
+        $force_discrete
+        #if $hpd2d_options.hpd2d_selector == 'set_hpd':
+            -hpd2D $hpd2d_options.hpd2d_value
+        #elif $hpd2d_options.hpd2d_selector == 'no_hpd':
+            -nohpd2D
+        #end if
+        $no_sa
+        '$input'
+        '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="beast.trees" label="Input tree file" help="File containing a sample of trees (from BEAST MCMC output)"/>
+        <param argument="-heights" type="select" label="Node heights" help="How to summarize node heights across trees">
+            <option value="keep" selected="true">Keep target tree heights</option>
+            <option value="median">Median heights</option>
+            <option value="mean">Mean heights</option>
+            <option value="ca">Common ancestor heights</option>
+        </param>
+        <conditional name="burnin_source">
+            <param name="burnin_selector" type="select" label="Specify burn-in">
+                <option value="percentage">Specify burn-in percentage</option>
+                <option value="none" selected="true">No burn-in (use all trees)</option>
+            </param>
+            <when value="percentage">
+                <param name="burnin_percent" type="integer" value="10" min="0" max="100" label="Burn-in percentage" help="Percentage of trees to discard as burn-in"/>
+            </when>
+            <when value="none"/>
+        </conditional>
+        <param argument="-limit" type="float" optional="true" min="0" max="1" label="Posterior probability limit" help="Minimum posterior probability for a node to be annotated (optional)"/>
+        <param argument="-target" type="data" format="txt,nhx,nex" optional="true" label="Target tree" help="Optional user-specified target tree to be annotated"/>    
+        <param argument="-force_discrete" type="boolean" truevalue="-forceDiscrete" falsevalue="" label="Force discrete traits" help="Forces integer traits to be treated as discrete traits"/>
+        <conditional name="hpd2d_options">
+            <param name="hpd2d_selector" type="select" label="Bivariate trait HPD options">
+                <option value="default" selected="true">Use default HPD settings</option>
+                <option value="set_hpd">Set custom HPD interval</option>
+                <option value="no_hpd">Suppress HPD calculation</option>
+            </param>
+            <when value="default"/>
+            <when value="set_hpd">
+                <param name="hpd2d_value" type="float" value="0.95" min="0" max="1" label="HPD interval for bivariate traits" help="The HPD (Highest Posterior Density) interval to be used"/>
+            </when>
+            <when value="no_hpd"/>
+        </conditional>
+        <param argument="no_sa" type="boolean" truevalue="-noSA" falsevalue="" label="Not sampled ancestor analysis" help="Interpret the tree set as NOT being from a sampled ancestor analysis, even if there are zero branch lengths"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="nhx" label="${tool.name} on ${on_string}: Annotated tree"/>
+    </outputs>
+
+    <tests>
+        <!-- Testing -height option -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input.trees"/>
+            <param name="heights" value="keep"/>
+            <output name="output" file="output.trees" compare="sim_size"/>
+        </test>
+        <!-- Testing -burnout option -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input.trees"/>
+            <param name="heights" value="median"/>
+            <conditional name="burnin_source">
+                <param name="burnin_selector" value="percentage"/>
+                <param name="burnin_percent" value="1"/>
+            </conditional>
+            <output name="output" file="output_burnout.trees" compare="sim_size"/>
+        </test>
+        <!-- Testing -limit option -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input.trees"/>
+            <param name="heights" value="mean"/>
+            <param name="limit" value="0.9"/>
+            <output name="output" file="output_limit.trees" compare="sim_size"/>
+        </test>
+        <!-- Testing -target option -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input.trees"/>
+            <param name="heights" value="ca"/>
+            <param name="target" value="target.trees"/>
+            <output name="output" file="output_target.trees" compare="sim_size"/>
+        </test>
+        <!-- Testing -hpd2D option -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input.trees"/>
+            <param name="heights" value="ca"/>
+            <conditional name="hpd2d_options">
+                <param name="hpd2d_selector" value="set_hpd"/>
+                <param name="hpd2d_value" value="0.95"/>
+            </conditional>
+            <output name="output" file="output_hpd.trees" compare="sim_size"/>
+        </test>
+        <!-- Testing -noSA option -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input.trees"/>
+            <param name="no_sa" value="true"/>
+            <output name="output" file="output_no_sa.trees" compare="sim_size"/>
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+**What it does**
+
+TreeAnnotator summarizes a sample of trees from a posterior distribution (those produced by BEAST) 
+into a single annotated tree. It can calculate summary statistics for node heights and other parameters, 
+and annotate the tree with posterior probabilities and other relevant information.
+
+**Input**
+
+The input should be a file containing multiple trees in Trees format typically from an MCMC analysis.
+
+**Options**
+
+- **Node heights**: Method for summarizing node heights across the tree sample
+  
+  - *Keep*: Retain the heights from a target tree
+  - *Median*: Use median heights across all trees
+  - *Mean*: Use mean heights across all trees  
+  - *Common ancestor (CA)*: Use heights from common ancestor nodes
+
+- **Burn-in**: Percentage of initial trees to discard as burn-in period
+
+- **Posterior probability limit**: Only annotate nodes with posterior probability above this threshold
+
+- **Target tree**: Optionally provide a specific tree topology to annotate
+
+- **Force discrete**: Treat integer-valued traits as discrete rather than continuous
+
+- **Bivariate HPD**: Options for calculating highest posterior density intervals for two-dimensional traits
+
+- **Not sampled ancestor**: Use when trees are not from sampled ancestor analysis
+
+**Output**
+
+A single annotated tree file containing summary information from the posterior tree distribution.
+
+    ]]></help>
+    <expand macro="citations"/>
+    <expand macro="creator"/>
+</tool>
\ No newline at end of file

From f684c0e4b7c39b88c33ca872ec4c83cae9d2b34f Mon Sep 17 00:00:00 2001
From: Saim Momin <mominsaim12@gmail.com>
Date: Fri, 24 Oct 2025 21:05:14 +0200
Subject: [PATCH 2/3] Correct output data format

---
 tools/beast2/treeannotator.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/beast2/treeannotator.xml b/tools/beast2/treeannotator.xml
index f99340fe066..680c763b232 100644
--- a/tools/beast2/treeannotator.xml
+++ b/tools/beast2/treeannotator.xml
@@ -63,7 +63,7 @@
         <param argument="no_sa" type="boolean" truevalue="-noSA" falsevalue="" label="Not sampled ancestor analysis" help="Interpret the tree set as NOT being from a sampled ancestor analysis, even if there are zero branch lengths"/>
     </inputs>
     <outputs>
-        <data name="output" format="nhx" label="${tool.name} on ${on_string}: Annotated tree"/>
+        <data name="output" format="beast.trees" label="${tool.name} on ${on_string}: Annotated tree"/>
     </outputs>
 
     <tests>

From ea49c055c2be3cada53d4611212e3dfad0d5e63f Mon Sep 17 00:00:00 2001
From: Saim Momin <mominsaim12@gmail.com>
Date: Fri, 24 Oct 2025 21:10:17 +0200
Subject: [PATCH 3/3] Change sim_size to diff

---
 tools/beast2/treeannotator.xml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/tools/beast2/treeannotator.xml b/tools/beast2/treeannotator.xml
index 680c763b232..5cea8f074cb 100644
--- a/tools/beast2/treeannotator.xml
+++ b/tools/beast2/treeannotator.xml
@@ -71,7 +71,7 @@
         <test expect_num_outputs="1">
             <param name="input" value="input.trees"/>
             <param name="heights" value="keep"/>
-            <output name="output" file="output.trees" compare="sim_size"/>
+            <output name="output" file="output.trees" compare="diff"/>
         </test>
         <!-- Testing -burnout option -->
         <test expect_num_outputs="1">
@@ -81,21 +81,21 @@
                 <param name="burnin_selector" value="percentage"/>
                 <param name="burnin_percent" value="1"/>
             </conditional>
-            <output name="output" file="output_burnout.trees" compare="sim_size"/>
+            <output name="output" file="output_burnout.trees" compare="diff"/>
         </test>
         <!-- Testing -limit option -->
         <test expect_num_outputs="1">
             <param name="input" value="input.trees"/>
             <param name="heights" value="mean"/>
             <param name="limit" value="0.9"/>
-            <output name="output" file="output_limit.trees" compare="sim_size"/>
+            <output name="output" file="output_limit.trees" compare="diff"/>
         </test>
         <!-- Testing -target option -->
         <test expect_num_outputs="1">
             <param name="input" value="input.trees"/>
             <param name="heights" value="ca"/>
             <param name="target" value="target.trees"/>
-            <output name="output" file="output_target.trees" compare="sim_size"/>
+            <output name="output" file="output_target.trees" compare="diff"/>
         </test>
         <!-- Testing -hpd2D option -->
         <test expect_num_outputs="1">
@@ -105,13 +105,13 @@
                 <param name="hpd2d_selector" value="set_hpd"/>
                 <param name="hpd2d_value" value="0.95"/>
             </conditional>
-            <output name="output" file="output_hpd.trees" compare="sim_size"/>
+            <output name="output" file="output_hpd.trees" compare="diff"/>
         </test>
         <!-- Testing -noSA option -->
         <test expect_num_outputs="1">
             <param name="input" value="input.trees"/>
             <param name="no_sa" value="true"/>
-            <output name="output" file="output_no_sa.trees" compare="sim_size"/>
+            <output name="output" file="output_no_sa.trees" compare="diff"/>
         </test>
     </tests>