--- a/jbrowse.xml	Thu Apr 11 09:35:00 2019 -0400
+++ b/jbrowse.xml	Mon Apr 15 10:31:26 2019 -0400
@@ -210,6 +210,15 @@
                   #end for
                 </menus>
             #end if
+            #if str($track.data_format.data_format_select) in ["gene_calls", "pileup", "blast", "wiggle", "vcf"]:
+                <custom_config>
+                #for $custom_option in $track.data_format.jb_custom_config.option:
+                  <${custom_option.opt_key}>
+                    <${custom_option.opt_value.val_type}>${$custom_option.opt_value.val}</${custom_option.opt_value.val_type}>
+                  </${custom_option.opt_key}>
+                #end for
+                </custom_config>
+            #end if
 
             #if str($track.data_format.data_format_select) == "wiggle":
                 <wiggle>
@@ -318,7 +327,8 @@
         BlastView="${plugins.BlastView}"
         theme=""
         />
-</root>]]></configfile>
+</root>
+]]></configfile>
   </configfiles>
   <inputs>
     <conditional name="reference_genome">
@@ -431,11 +441,13 @@
                 <expand macro="color_selection"
                         token_scaling_lin_select="false"
                         token_scaling_log_select="true" />
+                <expand macro="track_custom_config" />
                 <expand macro="track_menu" />
                 <expand macro="track_display" />
             </when>
             <when value="vcf">
                 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
+                <expand macro="track_custom_config" />
                 <expand macro="track_display" />
             </when>
             <when value="gene_calls">
@@ -487,6 +499,7 @@
                         description="note,description"
                         height="10px"/>
                 <expand macro="color_selection" />
+                <expand macro="track_custom_config" />
                 <expand macro="track_menu" />
                 <expand macro="track_display" />
             </when>
@@ -503,6 +516,7 @@
                        type="integer"
                        help="Maximum size in bytes of BAM chunks that the browser will try to deal with. When this is exceeded, most tracks will display 'Too much data' message."
                        value="5000000" />
+                <expand macro="track_custom_config" />
                 <expand macro="track_display" />
             </when>
             <when value="wiggle">
@@ -545,6 +559,7 @@
                     help="MultiBigWig is a plugin to group multiple big-wig tracks in a more aesthetically pleasing format and to show data in a higher density display." />
 
                 <expand macro="color_selection_minmax" />
+                <expand macro="track_custom_config" />
                 <expand macro="track_display" />
             </when>
             <when value="rest">
@@ -642,7 +657,7 @@
       <param name="gencode" value="1" />
       <param name="standalone" value="Data Directory" />
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gencode/test-1.xml" lines_diff="14"/>
+      <output name="output" file="gencode/test-1.xml" lines_diff="16"/>
     </test>
     <test>
       <param name="reference_genome|genome_type_select" value="history"/>
@@ -650,7 +665,7 @@
       <param name="gencode" value="11" />
       <param name="standalone" value="Data Directory" />
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gencode/test.xml" lines_diff="14"/>
+      <output name="output" file="gencode/test.xml" lines_diff="16"/>
     </test>
     <test>
       <param name="reference_genome|genome_type_select" value="history"/>
@@ -846,7 +861,7 @@
       </repeat>
 
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gff3/test.xml" lines_diff="256" />
+      <output name="output" file="gff3/test.xml" lines_diff="170" />
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -909,7 +924,7 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="menus/test.xml" lines_diff="24"/>
+        <output name="output" file="menus/test.xml" lines_diff="44"/>
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -927,6 +942,7 @@
                         <param name="match_part_select" value="false"/>
                     </conditional>
                     <conditional name="track_config">
+                        <param name="track_class" value="JBrowse/View/Track/CanvasFeatures"/>
                         <section name="canvas_options">
                             <param name="transcriptType" value="transcript"/>
                             <param name="subParts" value="exon"/>
@@ -946,7 +962,59 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="track_config/test.xml" lines_diff="26"/>
+        <output name="output" file="track_config/test.xml" lines_diff="30"/>
+    </test>
+    <test>
+        <param name="reference_genome|genome_type_select" value="history"/>
+        <param name="reference_genome|genome" value="merlin.fa"/>
+        <param name="gencode" value="11" />
+        <param name="standalone" value="Data Directory" />
+
+        <repeat name="track_groups">
+            <param name="category" value="With custom track 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>
+                    <section name="jb_custom_config">
+                        <repeat name="option">
+                            <param name="opt_key" value="displayMode"/>
+                            <conditional name="opt_value">
+                                <param name="val_type" value="text"/>
+                                <param name="val" value="collapsed"/>
+                            </conditional>
+                        </repeat>
+                        <repeat name="option">
+                            <param name="opt_key" value="histograms.height"/>
+                            <conditional name="opt_value">
+                                <param name="val_type" value="integer"/>
+                                <param name="val" value="150"/>
+                            </conditional>
+                        </repeat>
+                        <repeat name="option">
+                            <param name="opt_key" value="maxFeatureScreenDensity"/>
+                            <conditional name="opt_value">
+                                <param name="val_type" value="float"/>
+                                <param name="val" value="0.1"/>
+                            </conditional>
+                        </repeat>
+                        <repeat name="option">
+                            <param name="opt_key" value="style.strandArrow"/>
+                            <conditional name="opt_value">
+                                <param name="val_type" value="boolean"/>
+                                <param name="val" value="false"/>
+                            </conditional>
+                        </repeat>
+                    </section>
+                </conditional>
+            </repeat>
+        </repeat>
+
+        <param name="uglyTestingHack" value="enabled" />
+        <output name="output" file="custom_config/test.xml" lines_diff="30"/>
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -965,7 +1033,7 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="bam/test.xml" lines_diff="48"/>
+        <output name="output" file="bam/test.xml" lines_diff="42"/>
     </test>
 
     <test>
@@ -975,7 +1043,7 @@
         <param name="gencode" value="1" />
         <param name="standalone" value="Data Directory" />
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="gencode/test-data_table.xml" lines_diff="6" />
+        <output name="output" file="gencode/test-data_table.xml" lines_diff="4" />
     </test>
 
     <test>
@@ -1022,7 +1090,7 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="endpoints/test.xml" lines_diff="48"/>
+        <output name="output" file="endpoints/test.xml" lines_diff="16"/>
     </test>
   </tests>
   <help><![CDATA[