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

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9

<?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>