galaxyproject · SaimMomin12 · Oct 24, 2025 · Oct 24, 2025 · Oct 24, 2025 · Dec 4, 2025
diff --git a/tools/beast2/.shed.yml 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 }}"
diff --git a/tools/beast2/logcombiner.xml b/tools/beast2/logcombiner.xml
@@ -0,0 +1,98 @@
+<tool id="beast2_logcombiner" name="BEAST2 LogCombiner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Combine multiple trace or tree log files into a single log file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        logcombiner
+        #for $log_file in $log
+            -log '$log_file'
+        #end for
+        -b $burnin
+        #if $resample
+            -resample $resample
+        #end if
+        #if $decimal
+            -decimal
+        #end if
+        #if $renumber
+            -renumber
+        #end if
+        -o '$output'
+    ]]></command>
+    <inputs>
+        <param argument="-log" type="data" format="beast.trees,tabular" multiple="true" label="Log files" help="Select one or more log files to combine (trace or tree logs)" />
+        <param name="burnin" type="integer" value="10" min="0" max="100" label="Burnin percentage" help="Percentage of lines in the log file considered to be burnin" />
+        <param argument="-resample" type="integer" optional="true" label="Resample states" help="Specify number of states to resample" />
+        <param argument="-decimal" type="boolean" checked="false" truevalue="-decimal" falsevalue="" label="Convert to decimal format" help="Convert numbers from scientific notation to decimal format" />
+        <param argument="-renumber" type="boolean" checked="false" truevalue="-renumber" falsevalue="" label="Renumber output states" help="Renumber the states in the output file" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}: Combined log"/>
+    </outputs>
+
+    <tests>
+        <!-- Test 1: Basic options -->
+        <test expect_num_outputs="1">
+            <param name="log" value="log1.log,log2.log,log3.log"/>
+            <output name="output" file="test1_logcombiner.log"/>
+        </test>
+        <!-- Test 2: Custom burnin percentage -->
+        <test expect_num_outputs="1">
+            <param name="log" value="log1.log,log2.log"/>
+            <param name="burnin" value="20" />
+            <output name="output" file="test2_logcombiner.log"/>
+        </test>
+        <!-- Test 3: Combine tree logs -->
+        <test expect_num_outputs="1">
+            <param name="log" value="trees1.trees,trees2.trees,trees3.trees"/>
+            <output name="output" file="test3_logcombiner.log"/>
+        </test>
+        <!-- Test 4: Resample States -->
+         <test expect_num_outputs="1">
+            <param name="log" value="log1.log,log2.log,log3.log"/>
+            <param name="resample" value="10" />
+            <output name="output" file="test4_logcombiner.log"/>
+        </test>
+        <!-- Test 5: Scientific to decimal conversion -->
+        <test expect_num_outputs="1">
+            <param name="log" value="trace_scientific.log"/>
+            <param name="decimal" value="true" />
+            <output name="output" file="test5_logcombiner.log"/>
+        </test>
+        <!-- Test 6: Combined Options -->
+        <test expect_num_outputs="1">
+            <param name="log" value="trace_scientific.log"/>
+            <param name="burnin" value="10" />
+            <param name="resample" value="8" />
+            <param name="decimal" value="true" />
+            <param name="renumber" value="true" />
+            <output name="output" file="test6_logcombiner.log"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+LogCombiner is a tool from the BEAST2 suite that combines multiple trace or tree log files into a single log file.
+
+This is useful when you have run multiple independent MCMC chains and want to combine them for analysis.
+
+**Inputs**
+
+- **Log files**: One or more log files (trace or tree logs) to combine
+- **Burnin percentage**: Percentage of lines to discard from the beginning of each log file (default: 10%)
+- **Resample states** : Number of states to resample from the combined logs
+- **Convert to decimal**: Convert scientific notation to decimal format
+- **Renumber states**: Renumber the states in the output sequentially
+
+**Output**
+
+A single combined log file containing the merged data from all input files (after burnin removal).
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1371/journal.pcbi.1006650</citation>
+    </citations>
+</tool>
diff --git a/tools/beast2/macros.xml b/tools/beast2/macros.xml
@@ -0,0 +1,29 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.6.3</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>
diff --git a/tools/beast2/test-data/input.trees 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
diff --git a/tools/beast2/test-data/log1.log b/tools/beast2/test-data/log1.log
@@ -0,0 +1,21 @@
+Sample  posterior       likelihood      prior   TreeHeight      kappa   alpha
+0       -1234.56        -1000.12        -234.44 5.67    2.34    0.89
+1000    -1230.45        -995.23 -235.22 5.65    2.36    0.91
+2000    -1228.34        -992.11 -236.23 5.63    2.38    0.90
+3000    -1225.67        -990.34 -235.33 5.61    2.35    0.92
+4000    -1223.45        -988.56 -234.89 5.59    2.37    0.89
+5000    -1221.23        -986.78 -234.45 5.57    2.39    0.91
+6000    -1219.12        -985.01 -234.11 5.55    2.36    0.90
+7000    -1217.89        -983.45 -234.44 5.53    2.38    0.92
+8000    -1216.34        -982.12 -234.22 5.51    2.35    0.88
+9000    -1215.23        -981.00 -234.23 5.49    2.37    0.91
+10000   -1214.56        -980.34 -234.22 5.48    2.36    0.90
+11000   -1213.45        -979.23 -234.22 5.47    2.38    0.89
+12000   -1212.67        -978.45 -234.22 5.46    2.35    0.92
+13000   -1211.89        -977.67 -234.22 5.45    2.37    0.91
+14000   -1211.23        -977.01 -234.22 5.44    2.36    0.90
+15000   -1210.67        -976.45 -234.22 5.43    2.38    0.89
+16000   -1210.12        -975.90 -234.22 5.42    2.35    0.91
+17000   -1209.67        -975.45 -234.22 5.41    2.37    0.90
+18000   -1209.23        -975.01 -234.22 5.40    2.36    0.92
+19000   -1208.89        -974.67 -234.22 5.39    2.38    0.89
diff --git a/tools/beast2/test-data/log2.log b/tools/beast2/test-data/log2.log
@@ -0,0 +1,21 @@
+Sample  posterior       likelihood      prior   TreeHeight      kappa   alpha
+0       -1235.67        -1001.23        -234.44 5.68    2.33    0.88
+1000    -1231.23        -996.01 -235.22 5.66    2.35    0.90
+2000    -1229.12        -993.67 -235.45 5.64    2.37    0.89
+3000    -1226.45        -991.23 -235.22 5.62    2.36    0.91
+4000    -1224.23        -989.45 -234.78 5.60    2.38    0.90
+5000    -1222.01        -987.67 -234.34 5.58    2.35    0.92
+6000    -1220.23        -986.01 -234.22 5.56    2.37    0.89
+7000    -1218.67        -984.45 -234.22 5.54    2.36    0.91
+8000    -1217.12        -983.12 -234.00 5.52    2.38    0.90
+9000    -1216.01        -982.01 -234.00 5.50    2.35    0.92
+10000   -1215.34        -981.34 -234.00 5.49    2.37    0.89
+11000   -1214.23        -980.23 -234.00 5.48    2.36    0.91
+12000   -1213.45        -979.45 -234.00 5.47    2.38    0.90
+13000   -1212.67        -978.67 -234.00 5.46    2.35    0.92
+14000   -1212.01        -978.01 -234.00 5.45    2.37    0.89
+15000   -1211.45        -977.45 -234.00 5.44    2.36    0.91
+16000   -1210.90        -976.90 -234.00 5.43    2.38    0.90
+17000   -1210.45        -976.45 -234.00 5.42    2.35    0.92
+18000   -1210.01        -976.01 -234.00 5.41    2.37    0.89
+19000   -1209.67        -975.67 -234.00 5.40    2.36    0.91
diff --git a/tools/beast2/test-data/log3.log b/tools/beast2/test-data/log3.log
@@ -0,0 +1,21 @@
+Sample  posterior       likelihood      prior   TreeHeight      kappa   alpha
+0       -1236.78        -1002.34        -234.44 5.69    2.32    0.87
+1000    -1232.34        -997.12 -235.22 5.67    2.34    0.89
+2000    -1230.23        -994.78 -235.45 5.65    2.36    0.88
+3000    -1227.56        -992.34 -235.22 5.63    2.35    0.90
+4000    -1225.34        -990.56 -234.78 5.61    2.37    0.89
+5000    -1223.12        -988.78 -234.34 5.59    2.34    0.91
+6000    -1221.34        -987.12 -234.22 5.57    2.36    0.88
+7000    -1219.78        -985.56 -234.22 5.55    2.35    0.90
+8000    -1218.23        -984.23 -234.00 5.53    2.37    0.89
+9000    -1217.12        -983.12 -234.00 5.51    2.34    0.91
+10000   -1216.45        -982.45 -234.00 5.50    2.36    0.88
+11000   -1215.34        -981.34 -234.00 5.49    2.35    0.90
+12000   -1214.56        -980.56 -234.00 5.48    2.37    0.89
+13000   -1213.78        -979.78 -234.00 5.47    2.34    0.91
+14000   -1213.12        -979.12 -234.00 5.46    2.36    0.88
+15000   -1212.56        -978.56 -234.00 5.45    2.35    0.90
+16000   -1212.01        -978.01 -234.00 5.44    2.37    0.89
+17000   -1211.56        -977.56 -234.00 5.43    2.34    0.91
+18000   -1211.12        -977.12 -234.00 5.42    2.36    0.88
+19000   -1210.78        -976.78 -234.00 5.41    2.35    0.90
diff --git a/tools/beast2/test-data/output.trees 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
@@ -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
@@ -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;