--- a/jbrowseArchiveCreator.xml	Thu Feb 15 17:05:05 2018 -0500
+++ b/jbrowseArchiveCreator.xml	Fri Apr 20 13:51:23 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.0.1">
+<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.1.1">
     <description>
         This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin
     </description>
@@ -10,7 +10,8 @@
         <requirement type="package" version="1.9">numpy</requirement>
         <requirement type="package" version="1.68">biopython</requirement>
         <requirement type="package" version="340">ucsc_hac</requirement>
-        <requirement type="package" version="1.12.4">jbrowse_tools</requirement>
+        <requirement type="package" version="1.13.1">jbrowse_tools</requirement>
+        <requirement type="package" version="1.0">gff3sort</requirement>
     </requirements>
 
     <stdio>
@@ -149,6 +150,8 @@
 
 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
 
+#silent $data_parameter_dict.update({"feature_tracks_type": str($advanced_options.feature_tracks_type)})
+
 with open(file_path, 'w') as f:
     json.dump($data_parameter_dict, f)
         </configfile>
@@ -328,9 +331,13 @@
                 <option value="off" selected="true">Hide advanced options</option>
                 <option value="on">Display advanced options</option>
             </param>
-            <!-- TODO: Avoid redundancy here -->
             <when value="on">
-                <param name="debug_mode" type="select" label="Activate debug mode"> 
+                <param name="feature_tracks_type" type="select" label="Choose JBrowse feature tracks type">
+                    <option value="CanvasFeatures" selected="true">CanvasFeatures</option>
+                    <option value="HTMLFeatures">HTMLFeatures (Create a large number of range-indexed static JSON files. Don't choose this option if you want to upload/transfer output JBrowse hub to CyVerse Data Store!)
+                    </option>
+                </param>
+                <param name="debug_mode" type="select" label="Activate debug mode">
                     <option value="false" selected="true">No</option>
                     <option value="true">Yes</option>
                     <help>
@@ -339,9 +346,8 @@
                 </param>
             </when>
             <when value="off">
-                <param name="debug_mode" type="hidden"
-                       value="false">
-                </param>
+                <param name="debug_mode" type="hidden" value="false" />
+                <param name="feature_tracks_type" type="hidden" value="CanvasFeatures" />
             </when>
         </conditional>
     </inputs>
@@ -353,15 +359,14 @@
         <test>
             <param name="genome_name" value="Dbia3"/>
             <param name="fasta_file" value="common/dbia3.fa"/>
-            <output name="output" file="only_genome/only_genome.html">
+            <output name="output" file="only_genome/${tool.name}.html">
                 <!-- Use macro to check the whole common structure without repeated code -->
                 <expand macro="verify_hub_structure_no_track" test="only_genome" />
             </output>
         </test>
     </tests>
     <help>
-        This Galaxy tool will create a jbrowse hub which including binary datasets and json datasets that can be used for
-        JBrowse visualization.
+        This Galaxy tool will prepare your files to be ready for visualization on JBrowse/Apollo.
     </help>
     <citations>
     </citations>