--- a/jbrowse.xml	Tue Nov 29 12:31:56 2016 -0500
+++ b/jbrowse.xml	Fri Dec 02 17:58:54 2016 -0500
@@ -216,7 +216,18 @@
                 </blast>
             #else if str($track.data_format.data_format_select) == "gene_calls":
                 <gff>
-                    <trackType>${track.data_format.track_class}</trackType>
+                    <trackType>${track.data_format.track_config.track_class}</trackType>
+                  #if $track.data_format.track_config.track_class == 'JBrowse/View/Track/CanvasFeatures':
+                    #if str($track.data_format.track_config.canvas_options.transcriptType) != "":
+                    <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
+                    #end if
+                    #if str($track.data_format.track_config.canvas_options.subParts) != "":
+                    <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
+                    #end if
+                    #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false":
+                    <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs>
+                    #end if
+                  #end if
                   #if $track.data_format.match_part.match_part_select:
                     <match>${track.data_format.match_part.name}</match>
                   #end if
@@ -381,10 +392,36 @@
 
                 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
 
-                <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
-                  <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
-                  <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option>
-                </param>
+                <conditional name="track_config">
+                    <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
+                        <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
+                        <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option>
+                    </param>
+                    <when value="JBrowse/View/Track/CanvasFeatures">
+                        <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false">
+                            <param label="Transcript type"
+                                   name="transcriptType"
+                                   type="text"
+                                   value=""
+                                   help="If your input files represents transcripts with features not named 'mRNA', give the alternate name here (e.g. 'transcript')"
+                                   optional="True"/>
+                            <param label="Subfeatures type"
+                                   name="subParts"
+                                   type="text"
+                                   value=""
+                                   help="If you have 'exons' but no corresponding 'CDS' features, specify here the subfeatures that should be displayed (e.g. 'exon')"
+                                   optional="True"/>
+                            <param label="Implied UTRs"
+                                   name="impliedUTRs"
+                                   type="boolean"
+                                   checked="false"
+                                   truevalue="true"
+                                   falsevalue="false"
+                                   help="Check this your input files does not contain UTR features, but the UTR can be 'implied' from the difference between the exon and CDS boundaries"/>
+                       </section>
+                   </when>
+                   <when value="JBrowse/View/Track/HTMLFeatures" />
+                </conditional>
                 <expand macro="track_styling" />
                 <expand macro="color_selection" />
                 <expand macro="track_menu" />
@@ -729,6 +766,43 @@
         <param name="uglyTestingHack" value="enabled" />
         <output name="output" file="menus/test.xml" lines_diff="6"/>
     </test>
+    <test>
+        <param name="reference_genome|genome_type_select" value="history"/>
+        <param name="reference_genome|genomes" value="merlin.fa"/>
+        <param name="gencode" value="11" />
+        <param name="standalone" value="Data Directory" />
+
+        <repeat name="track_groups">
+            <param name="category" value="With canvas config" />
+            <repeat name="data_tracks">
+                <conditional name="data_format">
+                    <param name="data_format_select" value="gene_calls"/>
+                    <param name="annotation" value="gff3/1.gff"/>
+                    <conditional name="match_part">
+                        <param name="match_part_select" value="false"/>
+                    </conditional>
+                    <conditional name="track_config">
+                        <section name="canvas_options">
+                            <param name="transcriptType" value="transcript"/>
+                            <param name="subParts" value="exon"/>
+                            <param name="impliedUTRs" value="true"/>
+                        </section>
+                    </conditional>
+                    <section name="jbcolor_scale">
+                        <conditional name="color_score">
+                            <param name="color_score_select" value="none"/>
+                        </conditional>
+                        <conditional name="color">
+                            <param name="color_select" value="automatic"/>
+                        </conditional>
+                    </section>
+                </conditional>
+            </repeat>
+        </repeat>
+
+        <param name="uglyTestingHack" value="enabled" />
+        <output name="output" file="track_config/test.xml" lines_diff="6"/>
+    </test>
   </tests>
   <help><![CDATA[
 JBrowse-in-Galaxy