# HG changeset patch
# User rdvelazquez
# Date 1551896519 18000
# Node ID f93eb6f0f46f37e749054c92446f69a5425bdf49
# Parent  789b15630f96f7ca65e7bfe71a1fdd6721c75a7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty

diff -r 789b15630f96 -r f93eb6f0f46f hyphy_sm19.xml
--- a/hyphy_sm19.xml	Wed Mar 06 11:16:56 2019 -0500
+++ b/hyphy_sm19.xml	Wed Mar 06 13:21:59 2019 -0500
@@ -1,15 +1,15 @@
 <?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>
-  <expand macro="requirements">
-    <requirement type="package" version="2.4.0">hyphy</requirement>
-  </expand>
-  <version_command><![CDATA[HYPHYMP < <(echo && echo) | head -n 1 | awk '{print $1}']]></version_command>
-  <command detect_errors="exit_code"><![CDATA[
+    <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 '$input_file' sm19_input.nhx &&
     @HYPHY_ENVIRONMENT@ HYPHYMP LIBPATH=\$HYPHY_LIB
@@ -19,67 +19,73 @@
         '${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="'"/>
-          </valid>
-          <mapping initial="none">
-            <add source="'" 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[
+    ]]>
+    </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>
+        ]]>
+    </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>