--- a/create_reference_dataset.xml	Wed May 06 14:31:57 2015 -0500
+++ b/create_reference_dataset.xml	Mon Jan 04 15:55:00 2016 -0500
@@ -1,16 +1,17 @@
-<tool id="create_defuse_reference" name="Create DeFuse Reference" version="1.6.1">
+<tool id="create_defuse_reference" name="Create DeFuse Reference" version="@DEFUSE_VERSION@.1">
  <description>create a defuse reference from Ensembl and UCSC sources</description>
- <requirements>
-  <requirement type="package" version="0.6.1">defuse</requirement>
-  <requirement type="package" version="0.1.18">samtools</requirement>
-  <requirement type="package" version="1.0.0">bowtie</requirement>
-  <requirement type="package" version="2013-05-09">gmap</requirement>
-  <requirement type="package" version="latest">kent</requirement>
- </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="defuse_requirement" />
+        <expand macro="mapping_requirements" />
+    </requirements>
   <command interpreter="command"> /bin/bash $defuse_script </command>
  <inputs>
   <conditional name="genome">
     <param name="choice" type="select" label="Select a Genome Build">
+      <option value="GRCh38">Homo_sapiens GRCh38  hg38</option>
       <option value="GRCh37">Homo_sapiens GRCh37  hg19</option>
       <option value="NCBI36">Homo_sapiens NCBI36 hg18</option>
       <option value="GRCm38">Mus_musculus GRCm38 mm10</option>
@@ -18,6 +19,20 @@
       <option value="Rnor_5.0">Rattus_norvegicus Rnor_5.0 rn5</option>
       <option value="user_specified">User specified</option>
     </param>
+    <when value="GRCh38">
+      <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
+      <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
+      <param name="ensembl_genome_version" type="hidden" value="GRCh38"/>
+      <param name="ensembl_version" type="hidden" value="80"/>
+      <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
+      <param name="ncbi_prefix" type="hidden" value="Hs"/>
+      <param name="ucsc_genome_version" type="hidden" value="hg38"/>
+      <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
+      <param name="mt_chromosome" type="hidden" value="MT"/>
+      <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
+      <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
+      <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
+    </when>
     <when value="GRCh37">
       <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
       <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
@@ -220,6 +235,9 @@
 gene_sources = $genome.gene_sources
 ig_gene_sources = $genome.ig_gene_sources
 rrna_gene_sources = $genome.rrna_gene_sources
+gene_biotypes = $genome.gene_sources
+ig_gene_biotypes = $genome.ig_gene_sources
+rrna_gene_biotypes = $genome.rrna_gene_sources
 
 #raw
 # Remove temp files
@@ -286,4 +304,5 @@
 The galaxy history will contain: the config.txt file that provides DeFuse with the reference data paths.  
 
  </help>
+    <expand macro="citations"/>
 </tool>