Mercurial > repos > fubar > jbrowse2

diff test-data/bw/test.xml @ 3:2de9f585505b 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/jbrowse2 commit b30d2e277cc360437a02fa812c577c0c8d997cff-dirty
author fubar
date Tue, 09 Jan 2024 02:35:52 +0000
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bw/test.xml	Tue Jan 09 02:35:52 2024 +0000
@@ -0,0 +1,149 @@
+<?xml version="1.0"?>
+<root>
+    <metadata>
+        <genomes>
+            <genome>test-data/merlin.fa</genome>
+        </genomes>
+        <general>
+            <defaultLocation></defaultLocation>
+            <trackPadding>40</trackPadding>
+            <shareLink>true</shareLink>
+            <aboutDescription></aboutDescription>
+            <show_tracklist>true</show_tracklist>
+            <show_nav>true</show_nav>
+            <show_overview>false</show_overview>
+            <show_menu>true</show_menu>
+            <hideGenomeOptions>false</hideGenomeOptions>
+        </general>
+    </metadata>
+    <tracks>
+        <track cat="Scaling" format="wiggle">
+            <files>
+                <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Auto Global"/>
+            </files>
+
+            <options>
+                <wiggle>
+                    <type>JBrowse/View/Track/Wiggle/XYPlot</type>
+                    <variance_band>true</variance_band>
+                    <autoscale>global</autoscale>
+                    <color_pos>__auto__</color_pos>
+                    <color_neg>__auto__</color_neg>
+                    <bicolor_pivot>zero</bicolor_pivot>
+                    <scale>linear</scale>
+                </wiggle>
+            </options>
+        </track>
+        <track cat="Scaling" format="wiggle">
+            <files>
+                <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Auto Local"/>
+            </files>
+
+            <options>
+                <wiggle>
+                    <type>JBrowse/View/Track/Wiggle/XYPlot</type>
+                    <variance_band>true</variance_band>
+                    <autoscale>local</autoscale>
+                    <color_pos>__auto__</color_pos>
+                    <color_neg>__auto__</color_neg>
+                    <bicolor_pivot>zero</bicolor_pivot>
+                    <scale>linear</scale>
+                </wiggle>
+            </options>
+        </track>
+        <track cat="Scaling" format="wiggle">
+            <files>
+                <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Manual"/>
+            </files>
+
+            <options>
+                <wiggle>
+                    <type>JBrowse/View/Track/Wiggle/XYPlot</type>
+                    <variance_band>false</variance_band>
+                    <autoscale>fixed</autoscale>
+                    <min>20</min>
+                    <max>60</max>
+                    <color_pos>__auto__</color_pos>
+                    <color_neg>__auto__</color_neg>
+                    <bicolor_pivot>zero</bicolor_pivot>
+                    <scale>linear</scale>
+                </wiggle>
+            </options>
+        </track>
+
+
+        <track cat="Colouring" format="wiggle">
+            <files>
+                <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Auto A"/>
+                <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Auto B"/>
+            </files>
+
+            <options>
+                <wiggle>
+                    <type>JBrowse/View/Track/Wiggle/XYPlot</type>
+                    <variance_band>false</variance_band>
+                    <autoscale>local</autoscale>
+
+                    <color_pos>__auto__</color_pos>
+                    <color_neg>__auto__</color_neg>
+                    <bicolor_pivot>mean</bicolor_pivot>
+                    <scale>linear</scale>
+                </wiggle>
+            </options>
+        </track>
+        <track cat="Colouring" format="wiggle">
+            <files>
+                <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Manual"/>
+            </files>
+
+            <options>
+                <wiggle>
+                    <type>JBrowse/View/Track/Wiggle/XYPlot</type>
+                    <variance_band>false</variance_band>
+                    <autoscale>local</autoscale>
+
+                    <color_pos>#0000ff</color_pos>
+                    <color_neg>#ff0000</color_neg>
+                    <bicolor_pivot>mean</bicolor_pivot>
+                    <scale>linear</scale>
+                </wiggle>
+            </options>
+        </track>
+        <track cat="Colouring" format="wiggle">
+            <files>
+                <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Manual - Inverted"/>
+            </files>
+
+            <options>
+                <wiggle>
+                    <type>JBrowse/View/Track/Wiggle/XYPlot</type>
+                    <variance_band>false</variance_band>
+                    <autoscale>local</autoscale>
+
+                    <color_pos>#ff0000</color_pos>
+                    <color_neg>#0000ff</color_neg>
+                    <bicolor_pivot>mean</bicolor_pivot>
+                    <scale>log</scale>
+                </wiggle>
+            </options>
+        </track>
+        <track cat="Colouring" format="wiggle">
+            <files>
+                <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Nonstandard Pivot"/>
+            </files>
+
+            <options>
+                <wiggle>
+                    <type>JBrowse/View/Track/Wiggle/XYPlot</type>
+                    <variance_band>false</variance_band>
+                    <autoscale>local</autoscale>
+
+                    <color_pos>#0000ff</color_pos>
+                    <color_neg>#ff0000</color_neg>
+                    <bicolor_pivot>100</bicolor_pivot>
+                    <scale>linear</scale>
+                </wiggle>
+            </options>
+        </track>
+    </tracks>
+</root>