--- a/get.sharedseqs.xml	Tue Sep 05 16:55:11 2017 -0400
+++ b/get.sharedseqs.xml	Tue Mar 20 22:23:51 2018 -0400
@@ -7,41 +7,48 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$infile.otu" infile_otu.dat &&
-        #if $infile.intype == "in_listgroup":
-            ln -s "$infile.group" infile.group.dat &&
-            ln -s "$infile.fasta" infile_fasta.dat &&
+## create symlinks to input datasets
+ln -s '$infile.otu' infile_otu.dat &&
+#if $infile.intype == "in_listgroup":
+    ln -s '$infile.group' infile.group.dat &&
+    ln -s '$infile.fasta' infile_fasta.dat &&
+    ln -s '$count_in' count_in.dat &&
+#end if
+
+echo 'get.sharedseqs(
+    #if $infile.intype == "in_listgroup":
+        list=infile_otu.dat
+
+        #if $group:
+            ,group=infile.group.dat
+        #elif $count_in:
+            ,count=count_in.dat
         #end if
 
-        echo 'get.sharedseqs(
-            #if $infile.intype == "in_listgroup":
-                list=infile_otu.dat
-                ,group=infile.group.dat
-                #if $infile.fasta:
-                    ,fasta=infile_fasta.dat
-                #end if
-            #else
-                shared=infile_otu.dat
-            #end if
-            #if $infile.label:
-                ,label=${ str($infile.label).replace(",","-") }
-            #end if
-            #if $infile.seqsfrom.selection == "unique" and $infile.seqsfrom.groups:
-                ,uniquegroups=${ str($infile.seqsfrom.groups).replace(",","-") }
-            #end if
-            #if $infile.seqsfrom.selection == "shared" and $infile.seqsfrom.groups:
-                ,sharedgroups=${ str($infile.seqsfrom.groups).replace(",","-") }
-            #end if
-            #if $output:
-                ,output=$output
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+        #if $infile.fasta:
+            ,fasta=infile_fasta.dat
+        #end if
+    #else
+        shared=infile_otu.dat
+    #end if
+    #if $infile.label:
+        ,label=${ str($infile.label).replace(",","-") }
+    #end if
+    #if $infile.seqsfrom.selection == "unique" and $infile.seqsfrom.groups:
+        ,uniquegroups=${ str($infile.seqsfrom.groups).replace(",","-") }
+    #end if
+    #if $infile.seqsfrom.selection == "shared" and $infile.seqsfrom.groups:
+        ,sharedgroups=${ str($infile.seqsfrom.groups).replace(",","-") }
+    #end if
+    #if $output:
+        ,output=$output
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="infile">
@@ -81,13 +88,16 @@
             </when>
             <when value="in_listgroup">
                 <param name="otu" type="data" format="mothur.list" label="list - OTU List or shared file"/>
-                <param name="label" type="select" optional="true"  multiple="true" label="label - Select OTU Labels to include" help="By default all are included if no selection is made">
+                <param name="label" type="select" optional="true"  multiple="true" label="label - Select OTU Labels to include"
+                    help="By default all are included if no selection is made">
                     <options>
                         <filter type="data_meta" ref="otu" key="labels"/>
                     </options>
                 </param>
                 <param name="group" type="data" format="mothur.groups" optional="true" label="group - not required if using a shared file"/>
-                <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Dataset" help="will output a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified"/>
+                <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+                <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Dataset"
+                    help="will output a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified"/>
                 <conditional name="seqsfrom">
                     <param name="selection" type="select" label="Select Groups" help="">
                         <option value="all" selected="true">None (use all groups)</option>
@@ -116,6 +126,7 @@
             <option value="" selected="true">default: (name group bin_number)</option>
             <option value="accnos">accnos (name)</option>
         </param>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -138,8 +149,9 @@
             <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
             <param name="selection" value="shared"/>
             <output_collection name="sharedseqs" count="35">
-                <element name="0.41.unique.forest-pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/>
+                <element name="0.41.unique.forest_pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with list and group file -->
@@ -147,8 +159,9 @@
             <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
             <param name="group" value="amazon.groups" ftype="mothur.groups"/>
             <output_collection name="sharedseqs" count="35">
-                <element name="0.41.unique.forest-pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/>
+                <element name="0.41.unique.forest_pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with shared seqs and subset of labels -->
@@ -158,8 +171,9 @@
             <param name="groups" value="forest,pasture"/>
             <param name="label" value="0.03,0.33,0.41"/>
             <output_collection name="sharedseqs" count="3">
-                <element name="0.41.forest-pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/>
+                <element name="0.41.forest_pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with unique seqs and subset of groups -->
@@ -170,6 +184,7 @@
             <output_collection name="sharedseqs" count="34">
                 <element name="0.41.unique.pasture" md5="f4735f56d96d13cd603ca0b11c4bc231" ftype="tabular"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with accnos output -->
@@ -177,8 +192,9 @@
             <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
             <param name="output" value="accnos"/>
             <output_collection name="sharedaccnos" count="35">
-                <element name="0.41.unique.forest-pasture" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.accnos"/>
+                <element name="0.41.unique.forest_pasture" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.accnos"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with fasta input and output -->
@@ -187,16 +203,16 @@
             <param name="group" value="amazon.groups" ftype="mothur.groups"/>
             <param name="fasta" value="amazon.fasta" ftype="fasta"/>
             <output_collection name="sharedseqs" count="35">
-                <element name="0.41.unique.forest-pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/>
+                <element name="0.41.unique.forest_pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/>
             </output_collection>
             <output_collection name="sharedfastas" count="35">
-                <element name="0.41.unique.forest-pasture" md5="fd4265d7c139d2d3acf8e19e6337ee28" ftype="fasta"/>
+                <element name="0.41.unique.forest_pasture" md5="fd4265d7c139d2d3acf8e19e6337ee28" ftype="fasta"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -207,7 +223,7 @@
 .. _get.sharedseqs: https://www.mothur.org/wiki/Get.sharedseqs
 
 v1.21.0: Updated to Mothur 1.33, added shared file option
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>