annotate test-data/bw/test.xml @ 6:79f7265f90bd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9-dirty

<?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>