--- a/jbrowse.xml	Fri Jan 29 13:27:30 2016 -0500
+++ b/jbrowse.xml	Sat Jun 25 15:06:43 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="jbrowse" name="JBrowse" version="0.4">
+<tool id="jbrowse" name="JBrowse" version="0.5">
   <description>genome browser</description>
   <macros>
     <import>macros.xml</import>
@@ -7,20 +7,27 @@
   <expand macro="stdio"/>
   <version_command>python jbrowse.py --version</version_command>
   <command><![CDATA[
-mkdir -p $output.files_path &&
+
+#if $action.action_select == "create":
+    mkdir -p $output.files_path;
+#else:
+    cp -R $action.update_jbrowse.extra_files_path $output.files_path;
+#end if
+
 ## Copy the XML file into the directory, mostly for debugging
 ## but nice if users want to reproduce locally
 cp $trackxml $output.files_path/galaxy.xml &&
 
 ## Once that's done, we run the python script to handle the real work
 python $__tool_directory__/jbrowse.py
-$trackxml
 
 --jbrowse \${JBROWSE_SOURCE_DIR}
 #if str($standalone) == "Complete":
     --standalone
 #end if
---outdir $output.files_path;
+
+--outdir $output.files_path
+$trackxml;
 
 #if str($standalone) == "Complete":
     mv $output.files_path/index.html $output;
@@ -65,15 +72,29 @@
     <metadata>
         <gencode>$gencode</gencode>
         <genomes>
-            #for $genome in $genomes:
+            #if str($action.genomes) != "None":
+            #for $genome in $action.genomes:
                 <genome>$genome</genome>
             #end for
+            #end if
         </genomes>
+        <general>
+            <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
+            <trackPadding>${jbgen.trackPadding}</trackPadding>
+
+            <shareLink>${jbgen.shareLink}</shareLink>
+            <aboutDescription>${jbgen.aboutDescription}</aboutDescription>
+            <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
+            <show_nav>${jbgen.show_nav}</show_nav>
+            <show_overview>${jbgen.show_overview}</show_overview>
+            <show_menu>${jbgen.show_menu}</show_menu>
+            <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
+        </general>
     </metadata>
     <tracks>
         #for $tg in $track_groups:
         #for $track in $tg.data_tracks:
-        <track cat="${tg.category}" format="${track.data_format.data_format_select}">
+        <track cat="${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}" />
@@ -174,10 +195,18 @@
                 </blast>
             #else if str($track.data_format.data_format_select) == "gene_calls":
                 <gff>
+                    <trackType>${track.data_format.track_class}</trackType>
                   #if $track.data_format.match_part.match_part_select:
                     <match>${track.data_format.match_part.name}</match>
                   #end if
                 </gff>
+##            #else if str($track.data_format.data_format_select) == "sparql":
+##                <sparql>
+##                    <url>${track.data_format.url}</url>
+##                    <label>${track.data_format.label}</label>
+##                    <!-- This is going to be an absolutey nightmare -->
+##                    <query>${track.data_format.query}</query>
+##                </sparql>
             #end if
             </options>
         </track>
@@ -189,11 +218,33 @@
       </configfile>
   </configfiles>
   <inputs>
-    <param label="Fasta Sequence(s)"
-           name="genomes"
-           type="data"
-           format="fasta"
-           multiple="True"/>
+    <conditional name="action" label="Action">
+        <param type="select" label="JBrowse-in-Galaxy Action" name="action_select">
+            <option value="create">New JBrowse Instance</option>
+            <option value="update">Update exising JBrowse Instance</option>
+        </param>
+        <when value="create">
+            <param label="Fasta Sequence(s)"
+                   name="genomes"
+                   type="data"
+                   format="fasta"
+                   multiple="True"/>
+       </when>
+        <when value="update">
+            <param label="Additional Fasta Sequence(s)"
+                   help="If sequences are selected, they will be added to the existing JBrowse instance. You should not select any sequences if you are simply updating an existing JBrowse instance which already has the required reference sequences."
+                   name="genomes"
+                   type="data"
+                   format="fasta"
+                   optional="True"
+                   multiple="True"/>
+            <param label="Previous JBrowse Instance"
+                   name="update_jbrowse"
+                   type="data"
+                   format="html" />
+        </when>
+    </conditional>
+
     <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">
@@ -231,6 +282,7 @@
                 <option value="blast">Blast XML</option>
                 <option value="wiggle">BigWig XY</option>
                 <option value="vcf">VCF SNPs</option>
+                <!--<option value="sparql">SPARQL</option>-->
             </param>
             <when value="blast">
                 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
@@ -262,9 +314,11 @@
                 <expand macro="color_selection"
                         token_scaling_lin_select="false"
                         token_scaling_log_select="true" />
+                <expand macro="track_display" />
             </when>
             <when value="vcf">
                 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
+                <expand macro="track_display" />
             </when>
             <when value="gene_calls">
                 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
@@ -284,8 +338,13 @@
                     </when>
                     <when value="false" />
                 </conditional>
+                <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>
                 <expand macro="track_styling" />
                 <expand macro="color_selection" />
+                <expand macro="track_display" />
             </when>
             <when value="pileup">
                 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
@@ -295,6 +354,7 @@
                        name="auto_snp"
                        truevalue="true"
                        falsevalue="false" />
+                <expand macro="track_display" />
             </when>
             <when value="wiggle">
                 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
@@ -328,11 +388,21 @@
                     </when>
                 </conditional>
                 <expand macro="color_selection_minmax" />
+                <expand macro="track_display" />
             </when>
+            <!--
+            <when value="sparql">
+                <param type="text" label="SPARQL Server URL" name="url" />
+                <param type="text" label="Track Label" name="key" value="SPARQL Genes" />
+                <param type="text" label="SPARQL Query" name="query" area="true" />
+                <expand macro="track_display" />
+            </when>
+            -->
         </conditional>
     </repeat>
     </repeat>
 
+    <expand macro="general_options" />
     <param type="hidden" name="uglyTestingHack" value="" />
   </inputs>
   <outputs>
@@ -440,6 +510,12 @@
 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