annotate test-data/gff3/test.xml @ 5:ae9382cfb6ac draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed

<?xml version="1.0"?>
<root>
    <metadata>
        <gencode>11</gencode>
        <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="Auto Coloured" format="gene_calls" visibility="default_on">
            <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>feature</description>
                    <label>name,id</label>
                    <height>100px</height>
                </style>
                <gff>
                </gff>
                <scaling>
                    <method>ignore</method>
                    <scheme>
                        <color>__auto__</color>
                    </scheme>
                </scaling>
            </options>
        </track>
        <track cat="Ignore Scale" format="gene_calls">
            <files>
                <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/>
            </files>

            <options>
                <style>
                    <className>feature</className>
                    <description>feature</description>
                    <label>name,id</label>
                    <height>100px</height>
                </style>
                <gff>
                </gff>
                <scaling>
                    <method>ignore</method>
                    <scheme>
                        <color>#ff00ff</color>
                    </scheme>
                </scaling>
            </options>
        </track>
        <track cat="Scaled Colour" format="gene_calls">
            <files>
                <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/>
            </files>

            <options>
                <style>
                    <className>feature</className>
                    <description>feature</description>
                    <label>name,id</label>
                    <height>100px</height>
                </style>
                <gff>
                </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">
            <files>
                <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds, Fixed Color"/>
            </files>

            <options>
                <style>
                    <className>feature</className>
                    <description>feature</description>
                    <label>name,id</label>
                    <height>100px</height>
                </style>
                <gff>
                </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">
            <files>
                <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/>
            </files>

            <options>
                <style>
                    <className>feature</className>
                    <description>feature</description>
                    <label>name,id</label>
                    <height>100px</height>
                </style>
                <gff>
                </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">
            <files>
                <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds, Fixed Color"/>
            </files>

            <options>
                <style>
                    <className>feature</className>
                    <description>feature</description>
                    <label>name,id</label>
                    <height>100px</height>
                </style>
                <gff>
                </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">
            <files>
                <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/>
            </files>

            <options>
                <style>
                    <className>feature</className>
                    <description>feature</description>
                    <label>name,id</label>
                    <height>100px</height>
                </style>
                <gff>
                </gff>
                <scaling>
                    <method>ignore</method>
                    <scheme>
                        <color>__auto__</color>
                    </scheme>
                </scaling>
            </options>
        </track>
        <track cat="Realistic" format="gene_calls">
            <files>
                <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/>
            </files>

            <options>
                <style>
                    <className>feature</className>
                    <description>feature</description>
                    <label>name,id</label>
                    <height>100px</height>
                </style>
                <gff>
                    <match>cDNA_match</match>
                </gff>
                <scaling>
                    <method>ignore</method>
                    <scheme>
                        <type>opacity</type>
                        <color>__auto__</color>
                    </scheme>
                </scaling>
            </options>
        </track>
    </tracks>
</root>