annotate test-data/blastxml/test.xml @ 26:08776ba76cf5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5

<?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="Blah" format="blast">
            <files>
                <trackFile path="test-data/blastxml/blast.xml" ext="blastxml" label="BlastP"/>
            </files>

            <options>
                <style>
                    <className>feature</className>
                    <description></description>
                    <label>Description</label>
                    <height>400px</height>
                </style>
                <blast>
                    <parent>test-data/blastxml/merlin.gff</parent>
                    <protein>true</protein>
                    <min_gap>10</min_gap>
                </blast>
                <scaling>
                    <method>score</method>
                    <algo>blast</algo>
                    <scales>
                        <type>__auto__</type>
                    </scales>
                    <scheme>
                        <type>opacity</type>
                        <color>__auto__</color>
                    </scheme>
                </scaling>
            </options>
        </track>
        <track cat="Blah" format="blast">
            <files>
                <trackFile path="test-data/blastxml/blast.xml" ext="blastxml" label="BlastP, min_gap=3"/>
            </files>

            <options>
                <style>
                    <className>feature</className>
                    <description></description>
                    <label>Description</label>
                    <height>400px</height>
                </style>
                <blast>
                    <parent>test-data/blastxml/merlin.gff</parent>
                    <protein>true</protein>
                    <min_gap>3</min_gap>
                </blast>
                <scaling>
                    <method>score</method>
                    <algo>blast</algo>
                    <scales>
                        <type>__auto__</type>
                    </scales>
                    <scheme>
                        <type>opacity</type>
                        <color>__auto__</color>
                    </scheme>
                </scaling>
            </options>
        </track>

        <track cat="Blah" format="blast">
            <files>
                <trackFile path="test-data/blastxml/blast-gene1.xml" ext="blastxml" label="Non protein match/matchpart"/>
            </files>

            <options>
                <style>
                    <className>feature</className>
                    <description></description>
                    <label>Description</label>
                    <height>400px</height>
                </style>
                <blast>
                    <parent>test-data/blastxml/merlin.gff</parent>
                    <min_gap>3</min_gap>
                </blast>
                <scaling>
                    <method>ignore</method>
                    <algo>linear</algo>
                    <scheme>
                        <type>opacity</type>
                        <color>__auto__</color>
                    </scheme>
                </scaling>
            </options>
        </track>

        <track cat="Blah" format="blast">
            <files>
                <trackFile path="test-data/blastxml/blastn-gene1.xml" ext="blastxml" label="Non protein match/matchpart, no parent"/>
            </files>

            <options>
                <style>
                    <className>feature</className>
                    <description></description>
                    <label>Description</label>
                    <height>400px</height>
                </style>
                <blast>
                    <min_gap>40</min_gap>
                </blast>
                <scaling>
                    <method>score</method>
                    <algo>blast</algo>
                    <scales>
                        <type>__auto__</type>
                    </scales>
                    <scheme>
                        <type>opacity</type>
                        <color>__auto__</color>
                    </scheme>
                </scaling>
            </options>
        </track>

    </tracks>
</root>