--- a/jbrowse.xml	Tue Apr 28 10:01:04 2020 -0400
+++ b/jbrowse.xml	Fri Aug 21 04:42:41 2020 -0400
@@ -22,14 +22,12 @@
 python '$__tool_directory__/jbrowse.py'
 
 --jbrowse \${JBROWSE_SOURCE_DIR}
-#if str($standalone) == "Complete":
-    --standalone
-#end if
+--standalone '$standalone'
 
 --outdir $output.files_path
 $trackxml &&
 
-#if str($standalone) == "Complete":
+#if str($standalone) != "data":
     cp $output.files_path/index.html $output;
 #else:
     cp $dummyIndex $output;
@@ -372,7 +370,11 @@
         </when>
     </conditional>
 
-    <param name="standalone" type="boolean" truevalue="Complete" falsevalue="Data Directory" checked="true" label="Produce Standalone Instance" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo"/>
+    <param name="standalone" label="Output JBrowse" type="select">
+        <option value="complete">Complete, for viewing and further local development (JBrowse, tools, documentation, etc.)</option>
+        <option value="minimal" selected="true">Minimal for viewing (Documentation removed)</option>
+        <option value="data">Data directory only (primarily for use with Apollo, requires extra steps to serve as website)</option>
+    </param>
 
     <param name="gencode" type="select" label="Genetic Code">
       <option value="1">1. The Standard Code</option>
@@ -669,7 +671,7 @@
       <param name="reference_genome|genome_type_select" value="history"/>
       <param name="reference_genome|genome" value="merlin.fa"/>
       <param name="gencode" value="1" />
-      <param name="standalone" value="Data Directory" />
+      <param name="standalone" value="data" />
       <param name="uglyTestingHack" value="enabled" />
       <output name="output" file="gencode/test-1.xml" lines_diff="16"/>
     </test>
@@ -677,7 +679,7 @@
       <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" />
+      <param name="standalone" value="data" />
       <param name="uglyTestingHack" value="enabled" />
       <output name="output" file="gencode/test.xml" lines_diff="16"/>
     </test>
@@ -685,7 +687,7 @@
       <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" />
+      <param name="standalone" value="data" />
       <repeat name="track_groups">
         <param name="category" value="Default" />
         <repeat name="data_tracks">
@@ -702,7 +704,7 @@
       <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" />
+      <param name="standalone" value="data" />
       <repeat name="track_groups">
         <param name="category" value="Auto Coloured" />
         <repeat name="data_tracks">
@@ -898,7 +900,7 @@
         <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" />
+        <param name="standalone" value="data" />
 
         <repeat name="track_groups">
             <param name="category" value="With menu or index" />
@@ -961,7 +963,7 @@
         <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" />
+        <param name="standalone" value="data" />
 
         <repeat name="track_groups">
             <param name="category" value="With canvas config" />
@@ -999,7 +1001,7 @@
         <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" />
+        <param name="standalone" value="data" />
 
         <repeat name="track_groups">
             <param name="category" value="With custom track config" />
@@ -1051,7 +1053,7 @@
         <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" />
+        <param name="standalone" value="data" />
 
         <repeat name="track_groups">
             <param name="category" value="Auto Coloured" />
@@ -1072,7 +1074,7 @@
         <param name="reference_genome|genome_type_select" value="indexed"/>
         <param name="reference_genome|genome" value="merlin"/>
         <param name="gencode" value="1" />
-        <param name="standalone" value="Data Directory" />
+        <param name="standalone" value="data" />
         <param name="uglyTestingHack" value="enabled" />
         <output name="output" file="gencode/test-data_table.xml" lines_diff="4" />
     </test>
@@ -1081,7 +1083,7 @@
         <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" />
+        <param name="standalone" value="data" />
 
         <repeat name="track_groups">
             <param name="category" value="External endpoints" />