--- a/get.groups.xml	Tue Sep 05 16:51:18 2017 -0400
+++ b/get.groups.xml	Tue Mar 20 22:15:38 2018 -0400
@@ -7,58 +7,69 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$group_in" group_in.dat &&
-        ln -s "$fasta_in" fasta_in.dat &&
-        ln -s "$name_in" name_in.dat &&
-        ln -s "$list_in" list_in.dat &&
-        ln -s "$shared_in" shared_in.dat &&
-        ln -s "$taxonomy_in" taxonomy_in.dat &&
-        ln -s "$design_in" design_in.dat &&
-        #if $groupnames.source == 'accnos':
-            ln -s "$groupnames.accnos" groupnames.accnos.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$group_in' group_in.dat &&
+ln -s '$fasta_in' fasta_in.dat &&
+ln -s '$name_in' name_in.dat &&
+ln -s '$list_in' list_in.dat &&
+ln -s '$shared_in' shared_in.dat &&
+ln -s '$taxonomy_in' taxonomy_in.dat &&
+ln -s '$design_in' design_in.dat &&
+ln -s '$column_in' column_in.dat &&
+ln -s '$phylip_in' phylip_in.dat &&
+#if $groupnames.source == 'accnos':
+    ln -s '$groupnames.accnos' groupnames.accnos.dat &&
+#end if
 
-        echo 'get.groups(
-            #if $group_in.is_of_type("mothur.groups"):
-                group=group_in.dat
-            #else
-                count=group_in.dat
-            #end if
-            #if $groupnames.source == 'groups':
-                #if $groupnames.groups:
-                    ,groups=${ str($groupnames.groups).replace(",","-") }
-                #end if
-            #else
-                ,accnos=groupnames.accnos.dat
-            #end if
-            #if $fasta_in:
-                ,fasta=fasta_in.dat
-            #end if
-            #if $name_in:
-                ,name=name_in.dat
-            #end if
-            #if $list_in:
-                ,list=list_in.dat
-            #end if
-            #if $shared_in:
-                ,shared=shared_in.dat
-            #end if
-            #if $taxonomy_in:
-                ,taxonomy=taxonomy_in.dat
-            #end if
-            #if $design_in:
-                ,design=design_in.dat
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'get.groups(
+    #if $group_in.is_of_type("mothur.groups"):
+        group=group_in.dat
+    #else
+        count=group_in.dat
+    #end if
+    #if $groupnames.source == 'groups':
+        #if $groupnames.groups:
+            ,groups=${ str($groupnames.groups).replace(",","-") }
+        #end if
+    #else
+        ,accnos=groupnames.accnos.dat
+    #end if
+    #if $fasta_in:
+        ,fasta=fasta_in.dat
+    #end if
+    #if $name_in:
+        ,name=name_in.dat
+    #end if
+    #if $list_in:
+        ,list=list_in.dat
+    #end if
+    #if $shared_in:
+        ,shared=shared_in.dat
+    #end if
+    #if $taxonomy_in:
+        ,taxonomy=taxonomy_in.dat
+    #end if
+    #if $design_in:
+        ,design=design_in.dat
+    #end if
+    #if $column_in:
+        ,column=column_in.dat
+    #end if
+    #if $phylip_in:
+        ,phylip=phylip_in.dat
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
-        <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count_table file"/>
+        <param name="group_in" type="data" format="mothur.groups,mothur.count_table" optional="true" label="group or count_table file"/>
+        <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
+        <param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping"
+            help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
         <conditional name="groupnames">
             <param name="source" type="select" label="Select Group Names from">
                 <option value="groups">A List of Group Names</option>
@@ -78,9 +89,12 @@
         <param name="fasta_in" type="data" format="fasta,mothur.align" optional="true" label="fasta - Fasta Sequences"/>
         <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
         <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
-        <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
         <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
-        <param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
+        <param name="phylip_in" type="data" format="mothur.lower.dist,mothur.square.dist" optional="true" label="phylip - Distance Matrix you would like to select distances from"
+            help="must be a phylip-formatted distance matrix"/>
+        <param name="column_in" type="data" format="mothur.pair.dist" optional="true" label="column - Distance Matrix you would like to select distances from"
+            help="must be a column-formatted distance matrix"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -110,6 +124,12 @@
         <data name="design_out" format="mothur.design" from_work_dir="design_in*.pick.*" label="${tool.name} on ${on_string}: pick.design">
             <filter>design_in</filter>
         </data>
+        <data name="phylip_out" format_source="phylip_in" from_work_dir="phylip_in*.pick.*" label="${tool.name} on ${on_string}: pick.phylip">
+            <filter>phylip_in</filter>
+        </data>
+        <data name="column_out" format="mothur.pair.dist" from_work_dir="column_in*.pick.*" label="${tool.name} on ${on_string}: pick.column">
+            <filter>column_in</filter>
+        </data>
     </outputs>
     <tests>
         <test><!-- test with group file -->
@@ -117,6 +137,7 @@
             <param name="source" value="groups"/>
             <param name="groups" value="forest,pasture"/>
             <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with accnos file -->
@@ -124,6 +145,7 @@
             <param name="source" value="accnos"/>
             <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/>
             <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with accnos file and most extra files-->
@@ -143,11 +165,32 @@
             <output_collection name="sharedfiles" count="36">
                 <element name="0.38" md5="3c78742e0a480ca3353f9b591fc9bf36" ftype="mothur.shared"/>
             </output_collection>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with distance matrix -->
+            <param name="group_in" value="amazon_withgroups.count_table" ftype="mothur.count_table"/>
+            <param name="source" value="accnos"/>
+            <param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/>
+            <param name="column_in" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
+            <param name="phylip_in" value="amazon.dist" ftype="mothur.square.dist"/>
+            <output name="column_out" ftype="mothur.pair.dist">
+                <assert_contents>
+                    <expand macro="test-column-format"/>
+                    <has_text text="U68589"/>
+                </assert_contents>
+            </output>
+            <output name="phylip_out" ftype="mothur.square.dist">
+                <assert_contents>
+                    <expand macro="test-dist-format"/>
+                    <has_text text="U68589"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -162,7 +205,6 @@
 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
 .. _get.groups: https://www.mothur.org/wiki/Get.groups
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>