New tool addition: Beast2 wrappers

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 }}"

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>

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

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;

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;

tools/beast2/test-data/output_hpd.trees

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+#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;

tools/beast2/test-data/output_limit.trees

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+#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;

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;

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;

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;