Mercurial > repos > eduardo > annotateviz

diff test-data/gff3/test.xml @ 0:7537482eed36 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty
author eduardo
date Sat, 17 Jun 2017 13:31:06 -0400
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gff3/test.xml	Sat Jun 17 13:31:06 2017 -0400
@@ -0,0 +1,271 @@
+<?xml version="1.0"?>
+<root>
+    <metadata>
+        <gencode>11</gencode>
+        <genomes>
+                  <genome>test-data/merlin.fa</genome>
+        </genomes>
+        <general>
+            <defaultLocation></defaultLocation>
+            <trackPadding>20</trackPadding>
+
+            <shareLink>true</shareLink>
+            <aboutDescription></aboutDescription>
+            <show_tracklist>true</show_tracklist>
+            <show_nav>true</show_nav>
+            <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_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"/>
+            </files>
+
+            <options>
+                <style>
+                    <className>feature</className>
+                    <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>
+            </options>
+        </track>
+        <track cat="Ignore Scale" format="gene_calls" visibility="default_off">
+            <files>
+              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/>
+            </files>
+
+            <options>
+                <style>
+                    <className>feature</className>
+                    <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>
+            </options>
+        </track>
+        <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
+            <files>
+              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/>
+            </files>
+
+            <options>
+                <style>
+                    <className>feature</className>
+                    <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>
+            </options>
+        </track>
+        <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"/>
+            </files>
+
+            <options>
+                <style>
+                    <className>feature</className>
+                    <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>
+            </options>
+        </track>
+        <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
+            <files>
+              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/>
+            </files>
+
+            <options>
+                <style>
+                    <className>feature</className>
+                    <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>
+            </options>
+        </track>
+        <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"/>
+            </files>
+
+            <options>
+                <style>
+                    <className>feature</className>
+                    <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>
+            </options>
+        </track>
+        <track cat="Realistic" format="gene_calls" visibility="default_off">
+            <files>
+              <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/>
+            </files>
+
+            <options>
+                <style>
+                    <className>feature</className>
+                    <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>
+            </options>
+        </track>
+        <track cat="Realistic" format="gene_calls" visibility="default_off">
+            <files>
+              <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/>
+            </files>
+
+            <options>
+                <style>
+                    <className>feature</className>
+                    <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>
+            </options>
+        </track>
+    </tracks>
+</root>