--- a/get.oturep.xml	Tue Sep 05 17:17:12 2017 -0400
+++ b/get.oturep.xml	Tue Mar 20 22:11:51 2018 -0400
@@ -7,77 +7,79 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
+
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
+#if $method_condition.method_switch == "distance":
+    ln -s '$method_condition.matrix_condition.dist' dist.dat &&
+    ln -s '$method_condition.matrix_condition.nameOrCount' nameOrCount.dat &&
+    ln -s '$method_condition.fasta' fasta.dat &&
+    #if $method_condition.pick.type == "yes":
+        ln -s '$method_condition.pick.group' group.dat &&
+    #end if
+#elif $method_condition.method_switch == "abundance":
+    ln -s '$method_condition.nameOrCount' nameOrCount.dat &&
+#end if
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
-        #if $method_condition.method_switch == "distance":
-            ln -s "$method_condition.matrix_condition.dist" dist.dat &&
-            ln -s "$method_condition.matrix_condition.nameOrCount" nameOrCount.dat &&
-            ln -s "$method_condition.fasta" fasta.dat &&
-            #if $method_condition.pick.type == "yes":
-                ln -s "$method_condition.pick.group" group.dat &&
-            #end if
-        #elif $method_condition.method_switch == "abundance":
-            ln -s "$method_condition.nameOrCount" nameOrCount.dat &&
-        #end if
-
-        echo 'get.oturep(
-            list=otu.dat,
-            #if $sorted:
-                sorted=$sorted,
-            #end if
-            #if $label:
-                label=${ str($label).replace(",","-") },
+echo 'get.oturep(
+    list=otu.dat,
+    #if $sorted:
+        sorted=$sorted,
+    #end if
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $method_condition.method_switch == "distance":
+        method=distance,
+        #if $method_condition.matrix_condition.matrix_format == "column":
+            column=dist.dat,
+            #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"):
+                name=nameOrCount.dat,
+            #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"):
+                count=nameOrCount.dat,
             #end if
-            #if $method_condition.method_switch == "distance":
-                method=distance,
-                #if $method_condition.matrix_condition.matrix_format == "column":
-                    column=dist.dat,
-                    #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"):
-                        name=nameOrCount.dat,
-                    #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"):
-                        count=nameOrCount.dat,
-                    #end if
-                #elif $method_condition.matrix_condition.matrix_format == "phylip":
-                    phylip=dist.dat,
-                    #if $method_condition.matrix_condition.nameOrCount:
-                        #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"):
-                            name=nameOrCount.dat,
-                        #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"):
-                            count=nameOrCount.dat,
-                        #end if
-                    #end if
-                #end if
-                #if $method_condition.fasta:
-                    fasta=fasta.dat,
-                #end if
-                #if $method_condition.pick.type == "yes":
-                    #if $method_condition.pick.group:
-                        group=group.dat,
-                    #end if
-                    #if $method_condition.pick.groups:
-                        groups=${ str($method_condition.pick.groups).replace(",","-") },
-                    #end if
-                #end if
-                large=$method_condition.large
-            #elif $method_condition.method_switch == "abundance":
-                method=abundance,
-                #if $method_condition.nameOrCount.is_of_type("mothur.names"):
-                    name=nameOrCount.dat
-                #elif $method_condition.nameOrCount.is_of_type("mothur.count_table"):
-                    count=nameOrCount.dat
+        #elif $method_condition.matrix_condition.matrix_format == "phylip":
+            phylip=dist.dat,
+            #if $method_condition.matrix_condition.nameOrCount:
+                #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"):
+                    name=nameOrCount.dat,
+                #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"):
+                    count=nameOrCount.dat,
                 #end if
             #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+        #end if
+        #if $method_condition.fasta:
+            fasta=fasta.dat,
+        #end if
+        #if $method_condition.pick.type == "yes":
+            #if $method_condition.pick.group:
+                group=group.dat,
+            #end if
+            #if $method_condition.pick.groups:
+                groups=${ str($method_condition.pick.groups).replace(",","-") },
+            #end if
+        #end if
+        large=$method_condition.large
+    #elif $method_condition.method_switch == "abundance":
+        method=abundance,
+        #if $method_condition.nameOrCount.is_of_type("mothur.names"):
+            name=nameOrCount.dat
+        #elif $method_condition.nameOrCount.is_of_type("mothur.count_table"):
+            count=nameOrCount.dat
+        #end if
+    #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"/>
         <conditional name="method_condition">
-            <param name="method_switch" type="select" label="Method to use for the selection of the representative sequences" help="The distance method finds the sequence with the smallest maximum distance to other sequences. The abundance method chooses the most abundant sequence in the OTU as the representative.">
+            <param name="method_switch" type="select" label="Method to use for the selection of the representative sequences"
+                help="The distance method finds the sequence with the smallest maximum distance to other sequences. The abundance
+                method chooses the most abundant sequence in the OTU as the representative.">
                 <option value="distance" selected="true">distance</option>
                 <option value="abundance">abundance</option>
             </param>
@@ -112,7 +114,8 @@
                         </param>
                     </when>
                 </conditional>
-                <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Distance Matrix is very Large" help="Set this parameter to Yes if your distance matric might not fit in RAM"/>
+                <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Distance Matrix is very Large"
+                    help="Set this parameter to Yes if your distance matric might not fit in RAM"/>
             </when>
             <when value="abundance">
                 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/>
@@ -128,6 +131,7 @@
             <option value="size">Bin Size</option>
             <option value="group">Group</option>
         </param>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -158,6 +162,7 @@
             <output_collection name="names_out" count="36">
                 <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <!-- test with distance / column / label select -->
@@ -171,6 +176,7 @@
             <output_collection name="names_out" count="4">
                 <element name="0.27" md5="be6dccdd3d4619c3ac465246c826209a" ftype="mothur.names"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <!-- test with distance / fasta / sorting -->
@@ -188,6 +194,7 @@
             <output_collection name="fasta_out" count="2">
                 <element name="0.27" md5="a9d9622b6f5fcbe8acdc05df5484ffc4" ftype="fasta"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <!-- test with distance / group file -->
@@ -204,6 +211,7 @@
             <output_collection name="names_out" count="8">
                 <element name="0.27.pasture" md5="34f87d93fd9ebbefed9754f627f502fd" ftype="mothur.names"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <!-- test with distance / count table -->
@@ -217,6 +225,7 @@
             <output_collection name="count_out" count="3">
                 <element name="0.27" md5="6b1afd712825af4bf8cb4ab8304df903" ftype="mothur.count_table"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <!-- test with abundance / count / label -->
@@ -234,11 +243,11 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -250,7 +259,7 @@
 .. _get.oturep: https://www.mothur.org/wiki/Get.oturep
 
 v1.23.0: Updated to Mothur 1.33, added count and method parameter
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>