--- a/get.otus.xml	Tue Sep 05 16:33:51 2017 -0400
+++ b/get.otus.xml	Wed Feb 14 09:19:54 2018 -0500
@@ -7,95 +7,149 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
-        ln -s "$group_in" group_in.dat &&
-        #if $groupnames.source == 'accnos':
-            ln -s "$groupnames.accnos_in" groupnames.accnos_in.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$accnos' accnos.dat &&
+#if $list:
+    ln -s '$list' list.dat &&
+#end if
+#if $shared:
+    ln -s '$shared' shared.dat &&
+#end if
+#if $constaxonomy:
+    ln -s '$constaxonomy' constaxonomy.dat &&
+#end if
+#if $corraxes:
+    ln -s '$corraxes' corraxes.dat &&
+#end if
+#if $otucorr:
+    ln -s '$otucorr' otucorr.dat &&
+#end if
 
-        echo 'get.otus(
-            list=otu.dat,
-            group=group_in.dat
-            #if $label:
-                ,label=${ str($label).replace(",","-") }
-            #end if
-            #if $groupnames.source == 'groups':
-                ,groups=${ str($groupnames.groups).replace(",","-") }
-            #else
-                ,accnos=groupnames.accnos_in.dat
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'get.otus(
+    #if $list
+        list=list.dat,
+    #end if
+    #if $shared
+        shared=shared.dat,
+    #end if
+    #if $corraxes:
+        corraxes=corraxes.dat,
+    #end if
+    #if $otucorr:
+        otucorr=otucorr.dat,
+    #end if
+    #if $constaxonomy
+        constaxonomy=constaxonomy.dat,
+    #end if
+    accnos=accnos.dat
+    #if $labelsource.label:
+        ,label=${ str($labelsource.label).replace(",","-") }
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
-        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
-        <param name="label" type="select" optional="true" multiple="false" label="label - OTU Label" help="select exactly one label. If none selected, the first label in your file will be used">
-            <expand macro="labeloptions"/>
-        </param>
-        <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/>
-        <conditional name="groupnames">
-            <param name="source" type="select" label="Select Group Names from">
-                <option value="groups">A List of Group Names</option>
-                <option value="accnos">A History Group Name Accnos Dataset</option>
+        <param argument="accnos" type="data" format="mothur.accnos" label="accnos - Group Names from your history"/>
+        <param argument="list" type="data" format="mothur.list" optional="true" label="OTU List"/>
+        <param argument="shared" type="data" format="mothur.shared" optional="true" label="OTU List OTU Shared file"/>
+        <param argument="constaxonomy" type="data" format="mothur.cons.taxonomy" optional="true" label="contaxonomy - consensus taxonomy"
+            help="The contaxonomy file is the taxonomy file outputted by classify.otu"/>
+        <param argument="otucorr" type="data" format="mothur.otu.corr" optional="true" label="OTU correlation file"
+            help="otu correlation coefficients are output by the otu.association command"/>
+        <param argument="corraxes" type="data" format="mothur.axes" optional="true" label="Correlation axes file"
+            help="correlation axes file is output by the corr.axes command"/>
+
+        <conditional name="labelsource">
+            <param name="source" type="select" label="Select a label from">
+                <option value="list"> OTU list file </option>
+                <option value="shared"> OTU shared file </option>
             </param>
-            <when value="groups">
-                <param name="groups" type="select" multiple="true" force_select="true" label="groups - Pick groups to include">
-                    <help>At least one group must be selected</help>
+            <when value="list">
+                <param argument="label" type="select" optional="true" multiple="false" label="label - OTU Label"
+                    help="select exactly one label. If none selected, the first label in your file will be used">
                     <options>
-                        <filter type="data_meta" ref="group_in" key="groups"/>
+                        <filter type="data_meta" ref="list" key="labels"/>
                     </options>
                 </param>
             </when>
-            <when value="accnos">
-                <param name="accnos_in" type="data" format="mothur.accnos" optional="true" label="accnos - Group Names from your history"/>
+            <when value="shared">
+                <param argument="label" type="select" optional="true" multiple="false" label="label - OTU Label"
+                    help="select exactly one label. If none selected, the first label in your file will be used">
+                    <options>
+                        <filter type="data_meta" ref="shared" key="labels"/>
+                    </options>
+                </param>
             </when>
         </conditional>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
-        <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups"/>
-        <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.*" label="${tool.name} on ${on_string}: pick.list"/>
+        <data name="list_out" format="mothur.list" from_work_dir="list*.pick.*" label="${tool.name} on ${on_string}: pick.list">
+            <filter> $list </filter>
+        </data>
+        <data name="shared_out" format="mothur.shared" from_work_dir="shared*.pick.*" label="${tool.name} on ${on_string}: pick.shared">
+            <filter> $shared </filter>
+        </data>
+        <data name="constaxonomy_out" format="mothur.cons.taxonomy" from_work_dir="constaxonomy*.pick.*" label="${tool.name} on ${on_string}: pick.cons.taxonomy">
+            <filter> $constaxonomy </filter>
+        </data>
+        <data name="otucorr_out" format="mothur.otu.corr" from_work_dir="otucorr*.pick.*" label="${tool.name} on ${on_string}: pick.otu.corr">
+            <filter> $otucorr </filter>
+        </data>
+        <data name="corraxes_out" format="mothur.axes" from_work_dir="corraxes*.pick.*" label="${tool.name} on ${on_string}: pick.axes">
+            <filter> $corraxes </filter>
+        </data>
     </outputs>
     <tests>
-        <test><!-- test with group file -->
-            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
-            <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
-            <param name="source" value="groups"/>
-            <param name="groups" value="forest,pasture"/>
-            <output name="list_out" md5="a771e0879bbb84e2764db70f66ae1277" ftype="mothur.list"/>
-            <output name="group_out" md5="954ef97da9dcd152b912bcda19a6f96c" ftype="mothur.groups"/>
+        <test><!-- test with list file input and default settings -->
+            <param name="list" value="amazon.an.list" ftype="mothur.list"/>
+            <param name="accnos" value="amazon.otus.accnos" ftype="mothur.accnos"/>
+            <output name="list_out" ftype="mothur.list">
+                <assert_contents>
+                    <expand macro="test-list-format"/>
+                    <has_text text="unique"/>
+                    <has_text text="Otu01"/>
+                    <has_text text="Otu17"/>
+                    <has_text text="Otu42"/>
+                    <not_has_text text="Otu43"/>
+                </assert_contents>
+            </output>
             <expand macro="logfile-test"/>
         </test>
-        <test><!-- test with accnos file and label select -->
-            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+        <test><!-- test with shared and otu.corr file and label select -->
+            <param name="shared" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="accnos" value="amazon.otus.accnos" ftype="mothur.accnos"/>
             <param name="label" value="0.03"/>
-            <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
-            <param name="source" value="accnos"/>
-            <param name="accnos_in" value="amazon.groupaccnos" ftype="mothur.accnos"/>
-            <output name="list_out" md5="2069739b1f7bbbe47cc237833450e57c" ftype="mothur.list"/>
-            <output name="group_out" md5="09ffabe975dc49f1bf251ea60c569526" ftype="mothur.groups"/>
+            <param name="source" value="shared"/>
+            <param name="otucorr" value="amazon.an.0.03.pearson.otu.corr" ftype="mothur.cons.taxonomy"/>
+            <output name="shared_out" ftype="mothur.shared">
+                <assert_contents>
+                    <expand macro="test-shared-format"/>
+                    <has_text text="0.03"/>
+                    <has_text text="Otu01"/>
+                    <has_text text="Otu17"/>
+                    <has_text text="Otu42"/>
+                    <not_has_text text="Otu43"/>
+                </assert_contents>
+            </output>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
 **Command Documentation**
 
-The get.otus_ command selects otus from a list_ containing sequences from a specific group or set of groups.
+The get.otus command selects otus from a given list.
 
 .. _list: https://www.mothur.org/wiki/List_file
 .. _get.otus: https://www.mothur.org/wiki/Get.otus
 
-v.1.20.0: Updated to Mothur 1.33
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>