--- a/make.contigs.xml	Tue Sep 05 16:41:00 2017 -0400
+++ b/make.contigs.xml	Wed Feb 14 09:54:16 2018 -0500
@@ -7,58 +7,59 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## Symlinks creation or On the fly creation of a combo file
-        #if $input_type.type == 'list_collection'
-            #for $pair in $input_type.list_paired_collection:
-                ln -s ${pair.forward} `basename ${pair.forward}` &&
-                ln -s ${pair.reverse} `basename ${pair.reverse}` &&
-                echo -e "${pair.name}\t`basename ${pair.forward}`\t`basename ${pair.reverse}`" >> combo_fastq.dat &&
-            #end for
-        #elif $input_type.type == 'simple_collection'
-            ln -s '$input_type.paired_collection.forward' ffastq.dat &&
-            ln -s '$input_type.paired_collection.reverse' rfastq.dat &&
-        #else
-            ln -s '$input_type.forward_fastq' ffastq.dat &&
-            ln -s '$input_type.reverse_fastq' rfastq.dat &&
-        #end if
+## Symlinks creation or On the fly creation of a combo file
+#if $input_type.type == 'list_collection'
+    #for $pair in $input_type.list_paired_collection:
+        ln -s ${pair.forward} `basename ${pair.forward}` &&
+        ln -s ${pair.reverse} `basename ${pair.reverse}` &&
+        echo -e "${pair.name}\t`basename ${pair.forward}`\t`basename ${pair.reverse}`" >> combo_fastq.dat &&
+    #end for
+#elif $input_type.type == 'simple_collection'
+    ln -s '$input_type.paired_collection.forward' ffastq.dat &&
+    ln -s '$input_type.paired_collection.reverse' rfastq.dat &&
+#else
+    ln -s '$input_type.forward_fastq' ffastq.dat &&
+    ln -s '$input_type.reverse_fastq' rfastq.dat &&
+#end if
 
-        #if $oligo.add == "yes":
-            ln -s '$oligo.oligos' oligo.oligos.dat &&
-            ln -s '$oligo.findex' oligo.findex.dat &&
-            ln -s '$oligo.rindex' oligo.rindex.dat &&
-        #end if
+#if $oligo.add == "yes":
+    ln -s '$oligo.oligos' oligo.oligos.dat &&
+    ln -s '$oligo.findex' oligo.findex.dat &&
+    ln -s '$oligo.rindex' oligo.rindex.dat &&
+#end if
 
-        echo 'make.contigs(
-            #if $input_type.type == 'list_collection':
-                file=combo_fastq.dat,
-            #else:
-                ffastq=ffastq.dat,
-                rfastq=rfastq.dat,
-            #end if
-            align=$align,
-            #if $oligo.add == "yes":
-                oligos=oligo.oligos.dat,
-                bdiffs=$oligo.bdiffs,
-                pdiffs=$oligo.pdiffs,
-                tdiffs=$oligo.tdiffs,
-                #if $oligo.findex:
-                    findex=oligo.findex.dat,
-                #end if
-                #if $oligo.rindex:
-                    rindex=oligo.rindex.dat,
-                #end if
-            #end if
-            match=$match,
-            mismatch=$mismatch,
-            gapopen=$gapopen,
-            gapextend=$gapextend,
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'make.contigs(
+    #if $input_type.type == 'list_collection':
+        file=combo_fastq.dat,
+    #else:
+        ffastq=ffastq.dat,
+        rfastq=rfastq.dat,
+    #end if
+    align=$align,
+    #if $oligo.add == "yes":
+        oligos=oligo.oligos.dat,
+        bdiffs=$oligo.bdiffs,
+        pdiffs=$oligo.pdiffs,
+        tdiffs=$oligo.tdiffs,
+        #if $oligo.findex:
+            findex=oligo.findex.dat,
+        #end if
+        #if $oligo.rindex:
+            rindex=oligo.rindex.dat,
+        #end if
+    #end if
+    match=$match,
+    mismatch=$mismatch,
+    gapopen=$gapopen,
+    gapextend=$gapextend,
+    rename=$rename
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input_type">
@@ -103,6 +104,9 @@
         <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
         <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
         <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
+        <param name="rename" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Renames sequences"
+            help="reduce file sizes and greatly reduce the size of the column formatted distance matrix downstream.
+            Uses the rename.seqs command to rename which creates a map file so you can revert to original names at any time"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -193,8 +197,7 @@
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -205,7 +208,7 @@
 .. _make.contigs: https://www.mothur.org/wiki/Make.contigs
 
 v.1.27.0: Updated to use Mothur 1.33. Added findex and rindex parmaeters, optionally used with the oligos file.
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>