--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hyphy_sm19.xml	Tue Mar 05 20:14:43 2019 -0500
@@ -0,0 +1,91 @@
+<?xml version="1.0"?>
+<tool id="hyphy_sm19" name="HyPhy-SM2019" version="2.4.0+galaxy0">
+    <description>- Partition Tree using Modified Slatkin-Maddison Test</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="2.4.0">hyphy</requirement>
+    </requirements>
+    <version_command><![CDATA[HYPHYMP < <(echo && echo) | head -n 1 | awk '{print $1}']]></version_command>
+    <command detect_errors="exit_code">
+    <![CDATA[
+    #set $count = len($partitions)
+    ln -s '$input_file' sm19_input.nhx &&
+    @HYPHY_ENVIRONMENT@ HYPHYMP LIBPATH=\$HYPHY_LIB
+    \$HYPHY_LIB/TemplateBatchFiles/SM-2019.bf `pwd`/sm19_input.nhx $count
+    #for $n, $partition in enumerate($partitions):
+        '${partition.label}'
+        '${partition.regex}'
+    #end for
+    $replicates
+    ]]>
+    </command>
+    <inputs>
+        <param name="input_file" type="data" format="nhx" label="Input tree" />
+        <repeat name="partitions" min="2" max="50" title="Partitions">
+            <param name="label" type="text" label="Partition label" />
+            <param name="regex" type="text" label="Regular expression">
+                <sanitizer>
+                    <valid initial="string.printable">
+                        <remove value="&apos;" />
+                    </valid>
+                    <mapping initial="none">
+                        <add source="&apos;" target="__sq__" />
+                    </mapping>
+                </sanitizer>
+            </param>
+        </repeat>
+        <param name="replicates" type="integer" min="1" max="1000000" value="100" />
+    </inputs>
+    <outputs>
+        <data name="sm19_output" format="json" from_work_dir="sm19_input.nhx.json" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="fasta" value="sm19-in1.nhx" />
+            <param name="replicates" value="1000" />
+            <repeat name="partitions">
+                <param name="label" value="Blood" />
+                <param name="regex" value="B[0-9]+"/>
+            </repeat>
+            <repeat name="partitions">
+                <param name="label" value="Semen" />
+                <param name="regex" value="S[0-9]+"/>
+            </repeat>
+            <output name="sm19_output" file="sm19-out1.json" compare="sim_size" />
+        </test>
+        <test>
+            <param name="input_file" ftype="fasta" value="sm19-in2.nhx" />
+            <param name="replicates" value="1000" />
+            <repeat name="partitions">
+                <param name="label" value="Blood" />
+                <param name="regex" value="B[0-9]+"/>
+            </repeat>
+            <repeat name="partitions">
+                <param name="label" value="Semen" />
+                <param name="regex" value="S[0-9]+"/>
+            </repeat>
+            <output name="sm19_output" file="sm19-out2.json" compare="sim_size" />
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+This analysis implements canonical and modified versions of the Slatkin-Maddison
+phylogeny based test for population segregation. The test estimates the minimum
+number of migration events using maximum parsimony, and then evaluating whether
+or not this number is lower than expected in a panmictic or unstructured
+population using permutation tests.
+        ]]>
+    </help>
+    <expand macro="citations">
+        <citation type="bibtex">
+            @UNPUBLISHED{slatkin,
+                author = "Slatkin M, Maddison WP",
+                title = "A cladistic measure of gene flow inferred from the phylogenies of alleles",
+                year = "1989",
+                note = "Genetics 123(3):603-613",
+                url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"}
+        </citation>
+    </expand>
+</tool>