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diff test-data/gff3/test.xml @ 8:ad4b9d7eae6a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
author iuc
date Tue, 29 Nov 2016 10:55:30 -0500
parents ae9382cfb6ac
children ff11d442feed
line wrap: on
line diff
--- a/test-data/gff3/test.xml	Sun Jun 26 10:50:15 2016 -0400
+++ b/test-data/gff3/test.xml	Tue Nov 29 10:55:30 2016 -0500
@@ -3,226 +3,268 @@
     <metadata>
         <gencode>11</gencode>
         <genomes>
-            <genome>test-data/merlin.fa</genome>
+                  <genome>test-data/merlin.fa</genome>
         </genomes>
         <general>
             <defaultLocation></defaultLocation>
-            <trackPadding>40</trackPadding>
+            <trackPadding>20</trackPadding>
+
             <shareLink>true</shareLink>
             <aboutDescription></aboutDescription>
             <show_tracklist>true</show_tracklist>
             <show_nav>true</show_nav>
-            <show_overview>false</show_overview>
+            <show_overview>true</show_overview>
             <show_menu>true</show_menu>
             <hideGenomeOptions>false</hideGenomeOptions>
         </general>
     </metadata>
     <tracks>
-        <track cat="Auto Coloured" format="gene_calls" visibility="default_on">
+        <track cat="Auto Coloured" format="gene_calls" visibility="default_off">
             <files>
-                <trackFile path="test-data/gff3/1.gff" ext="gff3" label="A"/>
-                <trackFile path="test-data/gff3/1.gff" ext="gff3" label="B"/>
-                <trackFile path="test-data/gff3/1.gff" ext="gff3" label="C"/>
-                <trackFile path="test-data/gff3/1.gff" ext="gff3" label="D"/>
+              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="A"/>
+              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="B"/>
+              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="C"/>
+              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="D"/>
             </files>
 
             <options>
                 <style>
                     <className>feature</className>
-                    <description>feature</description>
+                    <description>note,description</description>
                     <label>name,id</label>
                     <height>100px</height>
                 </style>
+                <scaling>
+                        <method>ignore</method>
+                        <scheme>
+                            <color>__auto__</color>
+                        </scheme>
+                </scaling>
+                <menus>
+                </menus>
+
                 <gff>
+                    <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
+                    <index>false</index>
                 </gff>
-                <scaling>
-                    <method>ignore</method>
-                    <scheme>
-                        <color>__auto__</color>
-                    </scheme>
-                </scaling>
             </options>
         </track>
-        <track cat="Ignore Scale" format="gene_calls">
+        <track cat="Ignore Scale" format="gene_calls" visibility="default_off">
             <files>
-                <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/>
+              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/>
             </files>
 
             <options>
                 <style>
                     <className>feature</className>
-                    <description>feature</description>
+                    <description>note,description</description>
                     <label>name,id</label>
                     <height>100px</height>
                 </style>
+                <scaling>
+                        <method>ignore</method>
+                        <scheme>
+                            <color>#ff00ff</color>
+                        </scheme>
+                </scaling>
+                <menus>
+                </menus>
+
                 <gff>
+                    <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
+                    <index>false</index>
                 </gff>
-                <scaling>
-                    <method>ignore</method>
-                    <scheme>
-                        <color>#ff00ff</color>
-                    </scheme>
-                </scaling>
             </options>
         </track>
-        <track cat="Scaled Colour" format="gene_calls">
+        <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-                <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/>
+              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/>
             </files>
 
             <options>
                 <style>
                     <className>feature</className>
-                    <description>feature</description>
+                    <description>note,description</description>
                     <label>name,id</label>
                     <height>100px</height>
                 </style>
+                <scaling>
+                        <method>score</method>
+                        <algo>linear</algo>
+                        <scales>
+                            <type>automatic</type>
+
+                        </scales>
+                        <scheme>
+                            <type>opacity</type>
+                            <color>__auto__</color>
+                        </scheme>
+                </scaling>
+                <menus>
+                </menus>
+
                 <gff>
+                    <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
+                    <index>false</index>
                 </gff>
-                <scaling>
-                    <method>score</method>
-                    <algo>linear</algo>
-                    <scales>
-                        <type>__auto__</type>
-                    </scales>
-                    <scheme>
-                        <type>opacity</type>
-                        <color>__auto__</color>
-                    </scheme>
-                </scaling>
             </options>
         </track>
-        <track cat="Scaled Colour" format="gene_calls">
+        <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-                <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds, Fixed Color"/>
+              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds, Fixed Color"/>
             </files>
 
             <options>
                 <style>
                     <className>feature</className>
-                    <description>feature</description>
+                    <description>note,description</description>
                     <label>name,id</label>
                     <height>100px</height>
                 </style>
+                <scaling>
+                        <method>score</method>
+                        <algo>linear</algo>
+                        <scales>
+                            <type>automatic</type>
+
+                        </scales>
+                        <scheme>
+                            <type>opacity</type>
+                            <color>#0000ff</color>
+                        </scheme>
+                </scaling>
+                <menus>
+                </menus>
+
                 <gff>
+                    <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
+                    <index>false</index>
                 </gff>
-                <scaling>
-                    <method>score</method>
-                    <algo>linear</algo>
-                    <scales>
-                        <type>__auto__</type>
-                    </scales>
-                    <scheme>
-                        <type>opacity</type>
-                        <color>#0000ff</color>
-                    </scheme>
-                </scaling>
             </options>
         </track>
-        <track cat="Scaled Colour" format="gene_calls">
+        <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-                <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/>
+              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/>
             </files>
 
             <options>
                 <style>
                     <className>feature</className>
-                    <description>feature</description>
+                    <description>note,description</description>
                     <label>name,id</label>
                     <height>100px</height>
                 </style>
+                <scaling>
+                        <method>score</method>
+                        <algo>linear</algo>
+                        <scales>
+                            <type>manual</type>
+
+                            <min>0</min>
+                            <max>1000</max>
+                        </scales>
+                        <scheme>
+                            <type>opacity</type>
+                            <color>__auto__</color>
+                        </scheme>
+                </scaling>
+                <menus>
+                </menus>
+
                 <gff>
+                    <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
+                    <index>false</index>
                 </gff>
-                <scaling>
-                    <method>score</method>
-                    <algo>linear</algo>
-                    <scales>
-                        <type>manual</type>
-                        <min>0</min>
-                        <max>1000</max>
-                    </scales>
-                    <scheme>
-                        <type>opacity</type>
-                        <color>__auto__</color>
-                    </scheme>
-                </scaling>
             </options>
         </track>
-        <track cat="Scaled Colour" format="gene_calls">
+        <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-                <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds, Fixed Color"/>
+              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds, Fixed Color"/>
             </files>
 
             <options>
                 <style>
                     <className>feature</className>
-                    <description>feature</description>
+                    <description>note,description</description>
                     <label>name,id</label>
                     <height>100px</height>
                 </style>
+                <scaling>
+                        <method>score</method>
+                        <algo>linear</algo>
+                        <scales>
+                            <type>manual</type>
+
+                            <min>0</min>
+                            <max>1000</max>
+                        </scales>
+                        <scheme>
+                            <type>opacity</type>
+                            <color>#ff0000</color>
+                        </scheme>
+                </scaling>
+                <menus>
+                </menus>
+
                 <gff>
+                    <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
+                    <index>false</index>
                 </gff>
-                <scaling>
-                    <method>score</method>
-                    <algo>linear</algo>
-                    <scales>
-                        <type>manual</type>
-                        <min>0</min>
-                        <max>1000</max>
-                    </scales>
-                    <scheme>
-                        <type>opacity</type>
-                        <color>#ff0000</color>
-                    </scheme>
-                </scaling>
             </options>
         </track>
-
-
-        <track cat="Realistic" format="gene_calls">
+        <track cat="Realistic" format="gene_calls" visibility="default_off">
             <files>
-                <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/>
+              <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/>
             </files>
 
             <options>
                 <style>
                     <className>feature</className>
-                    <description>feature</description>
+                    <description>note,description</description>
                     <label>name,id</label>
                     <height>100px</height>
                 </style>
+                <scaling>
+                        <method>ignore</method>
+                        <scheme>
+                            <color>__auto__</color>
+                        </scheme>
+                </scaling>
+                <menus>
+                </menus>
+
                 <gff>
+                    <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
+                    <index>false</index>
                 </gff>
-                <scaling>
-                    <method>ignore</method>
-                    <scheme>
-                        <color>__auto__</color>
-                    </scheme>
-                </scaling>
             </options>
         </track>
-        <track cat="Realistic" format="gene_calls">
+        <track cat="Realistic" format="gene_calls" visibility="default_off">
             <files>
-                <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/>
+              <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/>
             </files>
 
             <options>
                 <style>
                     <className>feature</className>
-                    <description>feature</description>
+                    <description>note,description</description>
                     <label>name,id</label>
                     <height>100px</height>
                 </style>
+                <scaling>
+                        <method>ignore</method>
+                        <scheme>
+                            <color>__auto__</color>
+                        </scheme>
+                </scaling>
+                <menus>
+                </menus>
+
                 <gff>
+                    <trackType>JBrowse/View/Track/CanvasFeatures</trackType>
                     <match>cDNA_match</match>
+                    <index>false</index>
                 </gff>
-                <scaling>
-                    <method>ignore</method>
-                    <scheme>
-                        <type>opacity</type>
-                        <color>__auto__</color>
-                    </scheme>
-                </scaling>
             </options>
         </track>
     </tracks>