--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make.design.xml	Fri May 19 04:58:48 2017 -0400
@@ -0,0 +1,65 @@
+<tool profile="16.07" id="mothur_make_design" name="Make Design" version="@WRAPPER_VERSION@.0">
+    <description>Assign groups to Sets</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        #for $grouping in $groupings:
+            #set grp_str = $grouping.groups.__str__
+            #if grp_str:
+                #for $grp in grp_str.split(','):
+                    echo -e "$grp\t$grouping.name" >> $design;
+                #end for
+            #end if
+        #end for
+    ]]></command>
+    <inputs>
+        <param name="source" type="data" format="mothur.shared,mothur.groups" label="Source containing groups"/>
+        <repeat name="groupings" title="Grouping">
+            <param name="name" type="text" label="Name for a new combined grouping"/>
+            <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping">
+                <options>
+                    <filter type="data_meta" ref="source" key="groups"/>
+                </options>
+            </param>
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="design" format="mothur.design" label="${tool.name} on ${on_string}: design"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="source" value="amazon.mothur.shared" ftype="mothur.shared"/>
+            <repeat name="groupings">
+                <param name="name" value="tardis"/>
+                <param name="groups" value="forest,pasture"/>
+            </repeat>
+            <repeat name="groupings">
+                <param name="name" value="dalek"/>
+                <param name="groups" value="pasture"/>
+            </repeat>
+            <output name="design" file="toymothur.design" ftype="mothur.design"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+Make Design creates a design file for use in mothur commands: merge.groups_, indicator_, and metastats_.
+A design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.
+
+.. _merge.groups: https://www.mothur.org/wiki/Merge.groups
+.. _indicator: https://www.mothur.org/wiki/Indicator
+.. _metastats: https://www.mothur.org/wiki/Metastats
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>