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view test-data/gff3/test.xml @ 21:1c718d8b3532 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9cac72c004cc7ef57be997e2fdafb3b1839a300f
author iuc
date Tue, 11 Sep 2018 07:11:44 -0400
parents ff11d442feed
children 1cfc579079a6
line wrap: on
line source

<?xml version="1.0"?>
<root>
    <metadata>
        <gencode>11</gencode>
        <genomes>
                  <genome path="/tmp/tmpnh6QWY/files/000/dataset_5.dat">
                    <metadata>
                      <dataset id="7b55dbb89df8f4e5" hid="1"
                          size="171.6 KB"
                          edam_format="format_1929"
                          file_ext="fasta" />
                      <history id="54f2a3a23292eb07"
                          user_email="test@bx.psu.edu"
                          user_id="2"
                          display_name="test_history"/>
                      <metadata
                          dbkey="hg17"
                          data_lines="2881"
                          sequences="1"
                          />
                      <tool
                          tool_id="upload1"
                          tool_version="1.1.4"
                          />
                    </metadata>
                  </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>
        <galaxyUrl>http://localhost:8080</galaxyUrl>
    </metadata>
    <tracks>
        <track cat="Auto Coloured" format="gene_calls" visibility="default_off">
            <files>
              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_6.dat" ext="gff3" label="A.gff">
                <metadata>
                  <dataset id="fa6d20d0fb68383f" hid="2"
                      size="2.3 KB"
                      edam_format="format_1975"
                      file_ext="gff3" />
                  <history id="54f2a3a23292eb07"
                      user_email="test@bx.psu.edu"
                      user_id="2"
                      display_name="test_history"/>
                  <metadata
                      dbkey="hg17"
                      data_lines="27"
                      comment_lines="19"
                      columns="9"
                      column_names=""
                      delimiter="__tc__"
                      attributes="6"
                      />
                  <tool
                      tool_id="upload1"
                      tool_version="1.1.4"
                      />
                </metadata>
              </trackFile>
              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_7.dat" ext="gff3" label="B.gff">
                <metadata>
                  <dataset id="683bc220e21425bb" hid="3"
                      size="2.3 KB"
                      edam_format="format_1975"
                      file_ext="gff3" />
                  <history id="54f2a3a23292eb07"
                      user_email="test@bx.psu.edu"
                      user_id="2"
                      display_name="test_history"/>
                  <metadata
                      dbkey="hg17"
                      data_lines="27"
                      comment_lines="19"
                      columns="9"
                      column_names=""
                      delimiter="__tc__"
                      attributes="6"
                      />
                  <tool
                      tool_id="upload1"
                      tool_version="1.1.4"
                      />
                </metadata>
              </trackFile>
              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_8.dat" ext="gff3" label="C.gff">
                <metadata>
                  <dataset id="a90a30fafe298e1e" hid="4"
                      size="2.3 KB"
                      edam_format="format_1975"
                      file_ext="gff3" />
                  <history id="54f2a3a23292eb07"
                      user_email="test@bx.psu.edu"
                      user_id="2"
                      display_name="test_history"/>
                  <metadata
                      dbkey="hg17"
                      data_lines="27"
                      comment_lines="19"
                      columns="9"
                      column_names=""
                      delimiter="__tc__"
                      attributes="6"
                      />
                  <tool
                      tool_id="upload1"
                      tool_version="1.1.4"
                      />
                </metadata>
              </trackFile>
              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_9.dat" ext="gff3" label="D.gff">
                <metadata>
                  <dataset id="b842d972534ccb3e" hid="5"
                      size="2.3 KB"
                      edam_format="format_1975"
                      file_ext="gff3" />
                  <history id="54f2a3a23292eb07"
                      user_email="test@bx.psu.edu"
                      user_id="2"
                      display_name="test_history"/>
                  <metadata
                      dbkey="hg17"
                      data_lines="27"
                      comment_lines="19"
                      columns="9"
                      column_names=""
                      delimiter="__tc__"
                      attributes="6"
                      />
                  <tool
                      tool_id="upload1"
                      tool_version="1.1.4"
                      />
                </metadata>
              </trackFile>
            </files>

            <options>
                <style>
                    <overridePlugins>False</overridePlugins>
                    <overrideDraggable>False</overrideDraggable>
                    <className>feature</className>
                    <description>note,description</description>
                    <label>product,name,id</label>
                    <height>10px</height>
                    <maxHeight>600</maxHeight>
                </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="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
                <metadata>
                  <dataset id="5449172d6ff5669b" hid="6"
                      size="2.3 KB"
                      edam_format="format_1975"
                      file_ext="gff3" />
                  <history id="54f2a3a23292eb07"
                      user_email="test@bx.psu.edu"
                      user_id="2"
                      display_name="test_history"/>
                  <metadata
                      dbkey="hg17"
                      data_lines="27"
                      comment_lines="19"
                      columns="9"
                      column_names=""
                      delimiter="__tc__"
                      attributes="6"
                      />
                  <tool
                      tool_id="upload1"
                      tool_version="1.1.4"
                      />
                </metadata>
              </trackFile>
            </files>

            <options>
                <style>
                    <overridePlugins>False</overridePlugins>
                    <overrideDraggable>False</overrideDraggable>
                    <className>feature</className>
                    <description>note,description</description>
                    <label>product,name,id</label>
                    <height>10px</height>
                    <maxHeight>600</maxHeight>
                </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="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
                <metadata>
                  <dataset id="5449172d6ff5669b" hid="6"
                      size="2.3 KB"
                      edam_format="format_1975"
                      file_ext="gff3" />
                  <history id="54f2a3a23292eb07"
                      user_email="test@bx.psu.edu"
                      user_id="2"
                      display_name="test_history"/>
                  <metadata
                      dbkey="hg17"
                      data_lines="27"
                      comment_lines="19"
                      columns="9"
                      column_names=""
                      delimiter="__tc__"
                      attributes="6"
                      />
                  <tool
                      tool_id="upload1"
                      tool_version="1.1.4"
                      />
                </metadata>
              </trackFile>
            </files>

            <options>
                <style>
                    <overridePlugins>False</overridePlugins>
                    <overrideDraggable>False</overrideDraggable>
                    <className>feature</className>
                    <description>note,description</description>
                    <label>product,name,id</label>
                    <height>10px</height>
                    <maxHeight>600</maxHeight>
                </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="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
                <metadata>
                  <dataset id="5449172d6ff5669b" hid="6"
                      size="2.3 KB"
                      edam_format="format_1975"
                      file_ext="gff3" />
                  <history id="54f2a3a23292eb07"
                      user_email="test@bx.psu.edu"
                      user_id="2"
                      display_name="test_history"/>
                  <metadata
                      dbkey="hg17"
                      data_lines="27"
                      comment_lines="19"
                      columns="9"
                      column_names=""
                      delimiter="__tc__"
                      attributes="6"
                      />
                  <tool
                      tool_id="upload1"
                      tool_version="1.1.4"
                      />
                </metadata>
              </trackFile>
            </files>

            <options>
                <style>
                    <overridePlugins>False</overridePlugins>
                    <overrideDraggable>False</overrideDraggable>
                    <className>feature</className>
                    <description>note,description</description>
                    <label>product,name,id</label>
                    <height>10px</height>
                    <maxHeight>600</maxHeight>
                </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="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
                <metadata>
                  <dataset id="5449172d6ff5669b" hid="6"
                      size="2.3 KB"
                      edam_format="format_1975"
                      file_ext="gff3" />
                  <history id="54f2a3a23292eb07"
                      user_email="test@bx.psu.edu"
                      user_id="2"
                      display_name="test_history"/>
                  <metadata
                      dbkey="hg17"
                      data_lines="27"
                      comment_lines="19"
                      columns="9"
                      column_names=""
                      delimiter="__tc__"
                      attributes="6"
                      />
                  <tool
                      tool_id="upload1"
                      tool_version="1.1.4"
                      />
                </metadata>
              </trackFile>
            </files>

            <options>
                <style>
                    <overridePlugins>False</overridePlugins>
                    <overrideDraggable>False</overrideDraggable>
                    <className>feature</className>
                    <description>note,description</description>
                    <label>product,name,id</label>
                    <height>10px</height>
                    <maxHeight>600</maxHeight>
                </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="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
                <metadata>
                  <dataset id="5449172d6ff5669b" hid="6"
                      size="2.3 KB"
                      edam_format="format_1975"
                      file_ext="gff3" />
                  <history id="54f2a3a23292eb07"
                      user_email="test@bx.psu.edu"
                      user_id="2"
                      display_name="test_history"/>
                  <metadata
                      dbkey="hg17"
                      data_lines="27"
                      comment_lines="19"
                      columns="9"
                      column_names=""
                      delimiter="__tc__"
                      attributes="6"
                      />
                  <tool
                      tool_id="upload1"
                      tool_version="1.1.4"
                      />
                </metadata>
              </trackFile>
            </files>

            <options>
                <style>
                    <overridePlugins>False</overridePlugins>
                    <overrideDraggable>False</overrideDraggable>
                    <className>feature</className>
                    <description>note,description</description>
                    <label>product,name,id</label>
                    <height>10px</height>
                    <maxHeight>600</maxHeight>
                </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="/tmp/tmpnh6QWY/files/000/dataset_11.dat" ext="gff3" label="interpro.gff">
                <metadata>
                  <dataset id="9ce08b2254e4d5ed" hid="7"
                      size="103.3 KB"
                      edam_format="format_1975"
                      file_ext="gff3" />
                  <history id="54f2a3a23292eb07"
                      user_email="test@bx.psu.edu"
                      user_id="2"
                      display_name="test_history"/>
                  <metadata
                      dbkey="hg17"
                      data_lines="556"
                      comment_lines="2"
                      columns="9"
                      column_names=""
                      delimiter="__tc__"
                      attributes="11"
                      />
                  <tool
                      tool_id="upload1"
                      tool_version="1.1.4"
                      />
                </metadata>
              </trackFile>
            </files>

            <options>
                <style>
                    <overridePlugins>False</overridePlugins>
                    <overrideDraggable>False</overrideDraggable>
                    <className>feature</className>
                    <description>note,description</description>
                    <label>product,name,id</label>
                    <height>10px</height>
                    <maxHeight>600</maxHeight>
                </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="/tmp/tmpnh6QWY/files/000/dataset_12.dat" ext="gff3" label="2.gff">
                <metadata>
                  <dataset id="80b8022ff3f677b7" hid="8"
                      size="326 bytes"
                      edam_format="format_1975"
                      file_ext="gff3" />
                  <history id="54f2a3a23292eb07"
                      user_email="test@bx.psu.edu"
                      user_id="2"
                      display_name="test_history"/>
                  <metadata
                      dbkey="hg17"
                      data_lines="3"
                      comment_lines="3"
                      columns="9"
                      column_names=""
                      delimiter="__tc__"
                      attributes="4"
                      />
                  <tool
                      tool_id="upload1"
                      tool_version="1.1.4"
                      />
                </metadata>
              </trackFile>
            </files>

            <options>
                <style>
                    <overridePlugins>False</overridePlugins>
                    <overrideDraggable>False</overrideDraggable>
                    <className>feature</className>
                    <description>note,description</description>
                    <label>product,name,id</label>
                    <height>10px</height>
                    <maxHeight>600</maxHeight>
                </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>
    <plugins
        ComboTrackSelector=""
        Bookmarks=""
        GCContent=""
        theme=""
        />
</root>