--- a/macros.xml	Tue Jun 23 12:10:15 2015 -0400
+++ b/macros.xml	Thu Dec 31 13:58:43 2015 -0500
@@ -2,11 +2,13 @@
 <macros>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="1.11.6">jbrowse</requirement>
+      <requirement type="package" version="1.12.0">jbrowse</requirement>
+      <requirement type="package" version="1.12.0">bundle_jbrowse</requirement>
       <requirement type="package" version="2.7">python</requirement>
-      <requirement type="package" version="5.18">perl</requirement>
+      <requirement type="package" version="5.18.1">perl</requirement>
+      <requirement type="package" version="1.66">biopython</requirement>
+      <requirement type="package" version="0.6.2">bcbiogff</requirement>
       <requirement type="package" version="1.2">samtools</requirement>
-      <requirement type="package" version="1.0">bundle_jbrowse</requirement>
       <requirement type="package" version="3.11">pyyaml</requirement>
       <yield/>
     </requirements>
@@ -23,7 +25,203 @@
   <token name="@ATTRIBUTION@"><![CDATA[
 **Attribution**
 
-This Galaxy tool relies on the JBrowse, maintained by the GMOD Community
+This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche
 ]]>
   </token>
+  <xml name="auto_manual_tk"
+      token_cond_label="Color"
+      token_cond_name="color"
+      token_select_label="Color Specification"
+      token_select_name="color_select"
+      token_automatic_label="Automatically selected"
+      token_manual_label="Manual Color Selection">
+    <conditional name="@COND_NAME@" label="@COND_LABEL@">
+      <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@">
+        <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option>
+        <option value="manual">@MANUAL_LABEL@</option>
+      </param>
+      <when value="automatic">
+      </when>
+      <when value="manual">
+        <yield />
+      </when>
+    </conditional>
+  </xml>
+
+  <xml name="jb_color"
+      token_label="JBrowse style.color"
+      token_name="style_color"
+      token_value="goldenrod"
+      token_help="Basic color of features. Most glyphs interpret this as the fill color of the rectangle they draw. Color syntax is the same as that used for CSS"
+      >
+    <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
+      <sanitizer>
+        <valid initial="string.letters,string.digits">
+          <add value="#" />
+        </valid>
+      </sanitizer>
+    </param>
+  </xml>
+
+  <xml name="auto_color"
+       token_cond_label="Color"
+       token_cond_name="color"
+       token_select_label="Color Selection"
+       token_select_name="color_select"
+       token_automatic_label="Automatically selected"
+       token_manual_label="Manual Color Selection">
+    <expand macro="auto_manual_tk"
+            cond_label="@COND_LABEL@"
+            cond_name="@COND_NAME@"
+            select_label="@SELECT_LABEL@"
+            select_name="@SELECT_NAME@"
+            automatic_label="@AUTOMATIC_LABEL@"
+            manual_label="@MANUAL_LABEL@">
+      <expand macro="jb_color" />
+        <yield />
+    </expand>
+  </xml>
+
+
+
+  <xml name="brewer_scheme">
+    <param type="select" label="Brewer color Scheme" name="brewer_scheme">
+        <option value="BrBg">BrBg: Brown - Blue Green</option>
+        <option value="PiYg">PiYg: Pink - Yellow Green</option>
+        <option value="PRGn">PRGn: Purple Red - Green</option>
+        <option value="PuOr">PuOr: Purple - Orange</option>
+        <option value="RdBu" selected="true">RdBu: Red - Blue</option>
+        <option value="RdGy">RdGy: Red - Gray</option>
+        <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
+        <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
+        <option value="Spectral">Spectral</option>
+    </param>
+  </xml>
+  <xml name="color_selection_minmax">
+    <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false">
+      <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the
+           auto case as well, but may be safe to just say "brewer colors? Pff,
+           red/blue" -->
+      <expand macro="auto_manual_tk"
+              token_cond_label="Color"
+              token_cond_name="color"
+              token_select_label="Color Selection"
+              token_select_name="color_select"
+              token_automatic_label="Automatically selected"
+              token_manual_label="Manual Color Selection">
+        <expand macro="jb_color"
+                label="JBrowse style.pos_color"
+                name="style_pos_color"
+                value="blue"
+                help="CSS color, default 'blue'. When drawing bicolor plots, the fill color to use for values that are above the pivot point." />
+        <expand macro="jb_color"
+                label="JBrowse style.neg_color"
+                name="style_neg_color"
+                value="red"
+                help=" CSS color, default 'red'. When drawing bicolor plots, the fill color to use for values that are below the pivot point." />
+      </expand>
+
+      <conditional name="bicolor_pivot" label="Bicolor Pivot">
+        <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select">
+          <option value="zero" selected="true">Zero</option>
+          <option value="mean">Mean</option>
+          <option value="custom">Custom Value</option>
+        </param>
+        <when value="zero" />
+        <when value="mean" />
+        <when value="custom">
+          <param label="JBrowse style.bicolor_pivot" type="float" name="pivot_point" value="0.0" help="Where to change from pos_color to neg_color when drawing bicolor plots." />
+        </when>
+      </conditional>
+    </section>
+  </xml>
+
+  <xml name="color_selection"
+       token_scaling_lin_select="true"
+       token_scaling_log_select="false"
+      >
+    <section name="jbcolor_scale" title="JBrowse Feature Score Scaling &amp; Coloring Options [Advanced]" expanded="false">
+      <conditional name="color_score" label="JBrowse style.color &amp; Score relationship">
+        <param type="select" label="Color Score Algorithm" name="color_score_select" help="How to color the features. If it is based on score, then features with a score attribute anywhere in their hierachy will have their color affected by the score. If you choose to ignore the score, then you'll be able to select a single solid color for every feature in the track">
+          <option value="score">Based on score</option>
+          <option value="none" selected="true">Ignore score</option>
+        </param>
+        <when value="none">
+          <!-- When no scaling is done, no scores available, then just let the
+               user choose a base color for the track -->
+          <expand macro="auto_color" />
+        </when>
+        <when value="score">
+            <!-- Scaling -->
+            <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling"
+                   help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution.">
+              <option value="linear"      selected="@SCALING_LIN_SELECT@" >Linear scaling</option>
+              <option value="logarithmic" selected=""                     >Logarithmic scaling</option>
+              <option value="blast"       selected="@SCALING_LOG_SELECT@" >Blast scaling</option>
+            </param>
+
+            <!-- Scaling Bounds -->
+            <conditional name="score_scales" label="Minimum/Maximum values for track scores">
+              <param type="select" label="How should minimum and maximum values be determined for the scores of the features" name="scale_select">
+                <option value="automatic" selected="true">Automatically determined</option>
+                <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option>
+              </param>
+              <when value="automatic">
+              </when>
+              <when value="manual">
+                <param label="Minimum expected score" name="minimum" type="integer" value="0" />
+                <param label="Maximum expected score" name="maximum" type="integer" value="100" />
+              </when>
+            </conditional>
+
+            <!-- Scale color -->
+            <conditional name="color_scheme" label="Color Scheme for scored features">
+              <param type="select" label="JBrowse style.color function's color scheme for scored values" name="score_scheme">
+                <option value="opacity">Opacity (high scores = 1.0 opacity)</option>
+                <!--<option value="brewer">Brewer Color Schemes</option>-->
+              </param>
+              <when value="opacity">
+                <!-- Single color selection mode -->
+                <expand macro="auto_color" />
+              </when>
+              <!--<when value="brewer">-->
+                <!--[> Brewer continuum selection <]-->
+                <!--<expand macro="brewer_scheme" />-->
+              <!--</when>-->
+            </conditional>
+        </when>
+      </conditional>
+    </section>
+  </xml>
+  <xml name="track_styling"
+       token_classname="feature"
+       token_label="name,id"
+       token_description="note,description"
+       token_height="100px">
+    <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
+        <param label="JBrowse style.className" type="text"
+               name="style_classname"
+               value="@CLASSNAME@"
+               help="Set CSS style.className property"/>
+        <param label="JBrowse style.label"
+               type="text"
+               name="style_label"
+               value="@LABEL@"
+               help="Comma-separated list of case-insensitive feature tags to use for showing the feature's label. The first one found will be used. Default 'name,id'" />
+        <param label="JBrowse style.description"
+               type="text"
+               name="style_description"
+               value="@DESCRIPTION@"
+               help="Comma-separated list of case-insensitive feature tags to check for the feature's long description. The first one found will be used."/>
+        <param label="JBrowse style.height"
+               type="text"
+               name="style_height"
+               value="@HEIGHT@"
+               help="Height in pixels of glyphs. Default value varies from glyph to glyph. Note that the 'compact' displayMode uses style->height * 0.35 so changing style height can adjust the compact visualization."/>
+    </section>
+  </xml>
+
+  <xml name="input_conditional" token_label="Track Data" token_format="data">
+      <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
+  </xml>
 </macros>