--- a/jbrowse.xml	Wed Sep 13 13:07:20 2017 -0400
+++ b/jbrowse.xml	Wed Nov 15 15:15:27 2017 -0500
@@ -5,6 +5,7 @@
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
+  <version_command>python jbrowse.py --version</version_command>
   <command><![CDATA[
 
 #if $action.action_select == "create":
@@ -75,7 +76,29 @@
               <genome>${reference_genome.genomes.fields.path}</genome>
             #else
               #for $genome in $reference_genome.genomes:
-                  <genome>$genome</genome>
+                  <genome path="$genome">
+                    <metadata>
+                      <dataset id="${__app__.security.encode_id($genome.id)}" hid="${genome.hid}"
+                          size="${genome.get_size(nice_size=True)}"
+                          edam_format="${genome.datatype.edam_format}"
+                          file_ext="${genome.ext}" />
+                      <history id="${__app__.security.encode_id($genome.history_id)}"
+                          user_email="${genome.history.user.email}"
+                          user_id="${genome.history.user_id}"
+                          display_name="${genome.history.get_display_name()}"/>
+                      <metadata
+                          #for (key, value) in $genome.get_metadata().items():
+                          #if "_types" not in $key:
+                          ${key}="${value}"
+                          #end if
+                          #end for
+                          />
+                      <tool
+                          tool_id="${genome.creating_job.tool_id}"
+                          tool_version="${genome.creating_job.tool_version}"
+                          />
+                    </metadata>
+                  </genome>
               #end for
             #end if
         </genomes>
@@ -91,24 +114,55 @@
             <show_menu>${jbgen.show_menu}</show_menu>
             <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
         </general>
+        <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
     </metadata>
     <tracks>
         #for $tg in $track_groups:
         #for $track in $tg.data_tracks:
+        #if $track.data_format.data_format_select == "rest":
+        <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
+            <url>${track.data_format.url}</url>
+        </track>
+        #else:
         <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
             <files>
               #for $dataset in $track.data_format.annotation:
-              <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}" />
+              <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}">
+                <metadata>
+                  <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
+                      size="${dataset.get_size(nice_size=True)}"
+                      edam_format="${dataset.datatype.edam_format}"
+                      file_ext="${dataset.ext}" />
+                  <history id="${__app__.security.encode_id($dataset.history_id)}"
+                      user_email="${dataset.history.user.email}"
+                      user_id="${dataset.history.user_id}"
+                      display_name="${dataset.history.get_display_name()}"/>
+                  <metadata
+                    #for (key, value) in $dataset.get_metadata().items():
+                    #if "_types" not in $key:
+                      ${key}="${value}"
+                    #end if
+                    #end for
+                      />
+                  <tool
+                      tool_id="${dataset.creating_job.tool_id}"
+                      tool_version="${dataset.creating_job.tool_version}"
+                      />
+                </metadata>
+              </trackFile>
               #end for
             </files>
 
             <options>
             #if str($track.data_format.data_format_select) == "gene_calls" or  str($track.data_format.data_format_select) == "blast":
                 <style>
+                    <overridePlugins>${track.data_format.override_apollo_plugins}</overridePlugins>
+                    <overrideDraggable>${track.data_format.override_apollo_drag}</overrideDraggable>
                     <className>${track.data_format.jbstyle.style_classname}</className>
                     <description>${track.data_format.jbstyle.style_description}</description>
                     <label>${track.data_format.jbstyle.style_label}</label>
                     <height>${track.data_format.jbstyle.style_height}</height>
+                    <maxHeight>${track.data_format.jbstyle.max_height}</maxHeight>
                 </style>
                 <scaling>
                   #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
@@ -177,6 +231,7 @@
                     <min>${track.data_format.scaling.minimum}</min>
                     <max>${track.data_format.scaling.maximum}</max>
                   #end if
+                  <scale>${track.data_format.scale_select2}</scale>
 
                   ## Wiggle tracks need special color config
                   #if str($track.data_format.jbcolor.color.color_select) != "automatic":
@@ -247,11 +302,17 @@
             #end if
             </options>
         </track>
+        #end if
         #end for
         #end for
     </tracks>
-</root>
-]]></configfile>
+    <plugins
+        ComboTrackSelector="${plugins.ComboTrackSelector}"
+        Bookmarks="${plugins.Bookmarks}"
+        GCContent="${plugins.GCContent}"
+        theme="${plugins.theme}"
+        />
+</root>]]></configfile>
   </configfiles>
   <inputs>
     <conditional name="reference_genome">
@@ -284,7 +345,6 @@
 
     <param name="standalone" label="Produce Standalone Instance" type="boolean" truevalue="Complete" falsevalue="Data Directory" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo" checked="True"/>
 
-
     <param label="Genetic Code" name="gencode" type="select">
       <option value="1">1. The Standard Code</option>
       <option value="2">2. The Vertebrate Mitochondrial Code</option>
@@ -325,15 +385,16 @@
                name="category"
                type="text"
                value="Default"
-               help="Organise your tracks into Categories for a nicer end-user experience" optional="False"/>
+               help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/>
     <repeat name="data_tracks" title="Annotation Track">
-        <conditional name="data_format">
+        <conditional name="data_format" label="Track Options">
             <param type="select" label="Track Type" name="data_format_select">
                 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option>
                 <option value="pileup">BAM Pileups</option>
                 <option value="blast">Blast XML</option>
                 <option value="wiggle">BigWig XY</option>
                 <option value="vcf">VCF SNPs</option>
+                <option value="rest">REST Endpoint</option>
                 <!--<option value="sparql">SPARQL</option>-->
             </param>
             <when value="blast">
@@ -377,7 +438,7 @@
             </when>
             <when value="gene_calls">
                 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
-                <conditional name="match_part">
+                <conditional name="match_part" label="match/match_part data">
                     <param label="This is match/match_part data"
                            type="boolean"
                            name="match_part_select"
@@ -400,6 +461,7 @@
                     <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>
+                        <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option>
                     </param>
                     <when value="JBrowse/View/Track/CanvasFeatures">
                         <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false">
@@ -466,7 +528,7 @@
                        truevalue="true"
                        falsevalue="false" />
 
-                <conditional name="scaling">
+                <conditional name="scaling" label="Scaling">
                     <param type="select" label="Track Scaling" name="scale_select">
                         <option value="auto_local">Autoscale (local)</option>
                         <option value="auto_global" selected="true">Autoscale (global)</option>
@@ -481,9 +543,16 @@
                             type="integer" value="100" />
                     </when>
                 </conditional>
+                <param type="select" label="Visual Scaling" name="scale_select2">
+                    <option value="linear" selected="true">Linear</option>
+                    <option value="log">Logarithmic (Dynamically Calculated)</option>
+                </param>
                 <expand macro="color_selection_minmax" />
                 <expand macro="track_display" />
             </when>
+            <when value="rest">
+                <param type="text" label="REST Endpoint" name="url" />
+            </when>
             <!--
             <when value="sparql">
                 <param type="text" label="SPARQL Server URL" name="url" />
@@ -497,6 +566,25 @@
     </repeat>
 
     <expand macro="general_options" />
+    <section name="plugins" title="Plugins" expanded="false">
+        <param
+            label="Combo Track Selector" name="ComboTrackSelector" truevalue="True" falsevalue="" type="boolean"
+            help="ComboTrackSelector is a plugin to allow the co-existence of the Hierarchical and Faceted Track selectors in JBrowse, built for/by the Arabidopsis Information Portal (Araport) project" />
+        <param
+            label="Bookmarks" name="Bookmarks" truevalue="True" falsevalue="" type="boolean"
+            help="JBrowse plugin allowing users to manage a persistent list of bookmarks kept in localstorage" />
+
+        <param
+            label="GC Content" name="GCContent" truevalue="True" falsevalue="" type="boolean"
+            help="A JBrowse plugin for plotting GC Content and GC Skew. The plugin consists of a storeClass that automatically calculates the percentage of G/C bases in a region, a track type that derives from the Wiggle XY or density types, and a dialog box to adjust the sliding window size, window step size, and the calculation mode (content or skew)." />
+
+        <param type="select" label="JBrowse Theme" name="theme">
+            <option value="" selected="True">Default</option>
+            <option value="Minimalist">Minimalist</option>
+            <option value="Dark">Dark</option>
+        </param>
+    </section>
+
     <param type="hidden" name="uglyTestingHack" value="" />
   </inputs>
   <outputs>
@@ -518,7 +606,7 @@
       <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="4"/>
+      <output name="output" file="gencode/test.xml" lines_diff="14"/>
     </test>
     <test>
       <param name="reference_genome|genome_type_select" value="history"/>
@@ -714,7 +802,7 @@
       </repeat>
 
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gff3/test.xml" lines_diff="24" />
+      <output name="output" file="gff3/test.xml" lines_diff="64" />
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -777,7 +865,7 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="menus/test.xml" lines_diff="6"/>
+        <output name="output" file="menus/test.xml" lines_diff="24"/>
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -814,7 +902,7 @@
         </repeat>
 
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="track_config/test.xml" lines_diff="6"/>
+        <output name="output" file="track_config/test.xml" lines_diff="26"/>
     </test>
   </tests>
   <help><![CDATA[
@@ -824,6 +912,12 @@
 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
 alternative to Trackster.
 
+Overview
+--------
+
+JBrowse is a fast, embeddable genome browser built completely with
+JavaScript and HTML5.
+
 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
 JBrowse installations straight from Galaxy, taking advantage of the
 latest Galaxy features such as dataset collections, sections, and colour