--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge.groups.xml	Fri May 19 05:49:11 2017 -0400
@@ -0,0 +1,162 @@
+<tool profile="16.07" id="mothur_merge_groups" name="Merge.groups" version="@WRAPPER_VERSION@.0">
+    <description>Merge groups in a shared file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$otu" otu.dat &&
+        ln -s "$group" group.dat &&
+        #if $design.source == "hist":
+            ln -s "$design.design_dataset" design_dataset.dat &&
+        #else:
+            ln -s "$generated_design" generated_design.dat &&
+        #end if
+
+        echo 'merge.groups(
+            #if $design.source == "hist":
+                design=design_dataset.dat
+            #else:
+                design=generated_design.dat
+            #end if
+            #if $otu:
+                ,shared=otu.dat
+            #end if
+            #if $group:
+                ,group=group.dat
+            #end if
+            #if $groups:
+                ,groups=${ str($groups).replace(",","-") }
+            #end if
+            #if $label:
+                ,label=${ str($label).replace(",","-") }
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <configfiles>
+        <configfile name="generated_design"><![CDATA[
+            #if $design.source == 'build':
+                #for $grouping in $design.groupings:
+                    #set grp_str = $grouping.groups.__str__
+                    #if grp_str != None and len(grp_str) > 0:
+                        #for $grp in grp_str.split(','):
+                            $grp	$grouping.name
+                        #end for
+                    #end if
+                #end for
+            #end if
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="otu" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared Dataset"/>
+        <param name="label" type="select" label="label - Pick OTU Labels to include" optional="true" multiple="true">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="group" type="data" format="mothur.groups" optional="true" label="group - Group Dataset"/>
+        <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
+            <options>
+                <filter type="data_meta" ref="otu" key="groups"/>
+            </options>
+        </param>
+        <conditional name="design">
+            <param name="source" type="select" label="Grouping Design from" help="">
+                <option value="hist">Your History</option>
+                <option value="build">Build a grouping design</option>
+            </param>
+            <when value="hist">
+                <param name="design_dataset" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
+            </when>
+            <when value="build">
+                <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="otu" key="groups"/>
+                        </options>
+                    </param>
+                </repeat>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="merged_shared" format="mothur.shared" from_work_dir="otu*.merge.*" label="${tool.name} on ${on_string}: merge.shared">
+            <filter>otu</filter>
+        </data>
+        <data name="merged_group" format="mothur.groups" from_work_dir="group*.merge.*" label="${tool.name} on ${on_string}: merge.groups">
+            <filter>group</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test><!-- test with shared file -->
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="source" value="hist"/>
+            <param name="design_dataset" value="toymothur.design2"/>
+            <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with shared file and label and group select -->
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="label" value="0.05,0.22,0.38"/>
+            <param name="groups" value="forest,pasture"/>
+            <param name="source" value="hist"/>
+            <param name="design_dataset" value="toymothur.design2"/>
+            <output name="merged_shared" md5="11818d535bf88938dc063afca3f95b23" ftype="mothur.shared"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with group file -->
+            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
+            <param name="source" value="hist"/>
+            <param name="design_dataset" value="toymothur.design2"/>
+            <output name="merged_group" md5="023ebd0668522e9531da5b061e6e9137" ftype="mothur.groups"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with design creation -->
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="source" value="build"/>
+            <repeat name="groupings">
+                <param name="name" value="tardis"/>
+                <param name="groups" value="forest"/>
+            </repeat>
+            <repeat name="groupings">
+                <param name="name" value="dalek"/>
+                <param name="groups" value="pasture"/>
+            </repeat>
+            <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The merge.groups_ command reads a shared_ file and a design file and merges the groups in the shared file that are in the same grouping in the design file.
+
+A design file partitions a list of names into groups.  It is a tab-delimited file with 2 columns: name and group, e.g. :
+                                ======= =======
+                                duck    bird
+                                cow     mammal
+                                pig     mammal
+                                goose   bird
+                                cobra   reptile
+                                ======= =======
+
+The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
+
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _merge.groups: https://www.mothur.org/wiki/Merge.groups
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>