--- a/trinityrnaseq.xml	Fri Sep 23 10:01:55 2016 -0400
+++ b/trinityrnaseq.xml	Mon Sep 26 16:09:24 2016 -0400
@@ -14,16 +14,20 @@
     <command>
         MEM=`expr "\${GALAXY_SLOTS:-16}" \* 48 - 16` ;
 
-	workdir=`pwd`;
+        workdir=`pwd`;
         echo "workdir is \$workdir";
-	cd \$LOCAL;
-	echo "Running Trinity from `pwd`";
+        cd \$LOCAL;
+        echo "Running Trinity from `pwd`";
 
         Trinity --max_memory "\${MEM}G"
                 --CPU "\${GALAXY_SLOTS:-16}"
                 --bflyHeapSpaceMax "32G"
                 --bflyHeapSpaceInit "2G"
                 --bflyGCThreads "6"
+
+        #if $additional_params.use_additional == "yes" and $additional_params.normalize_reads == "yes":
+            --normalize_reads
+        #end if
         
         ## Inputs.
         #if str($inputs.paired_or_single) == "paired":
@@ -111,6 +115,8 @@
                 <param name="max_reads_per_graph" type="integer" value="20000000" min="10000" label="chrysalis_max_reads_per_graph" help="Maximum number of reads to be anchored within each transcript graph by Chrysalis" />
                 <param name="bfly_opts" type="text" value="None" label="bfly_opts" help="Options to pass on to Butterfly" />
                 <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/>
+                <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/>
+                <param name="normalize_reads" type="boolean" truevalue="yes" falsevalue="no" help="(--normalize_reads) Normalize reads, can decrease runtime and memory requirements for datasets exceeding 300M pairs"/>
             </when>
         </conditional>
     </inputs>