view test-data/bam/test.xml @ 40:17359b808b01 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"

<?xml version="1.0"?>
<root>
    <metadata>
        <gencode>11</gencode>
        <genomes>
              <genome path="/tmp/tmpqkd9zdgq/files/d/3/d/dataset_d3d20b83-6a77-4e76-bb7e-3b9fe7261453.dat">
                <metadata>
                  <dataset id="238993350abc9bfd" hid="1"
                      size="171.6 KB"
                      edam_format="format_1929"
                      file_ext="fasta" />
                  <history id="a90a30fafe298e1e"
                      user_email="[e-mail]"
                      user_id="2"
                      display_name="test_history"/>
                  <metadata
                      dbkey="?"
                      data_lines="2881"
                      sequences="1"
                      />
                  <tool
                      tool_id="upload1"
                      tool_version="1.1.6"
                      />
                </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</galaxyUrl>
    </metadata>
    <tracks>
        <track cat="Auto Coloured" format="pileup" visibility="default_off">
            <files>
              <trackFile path="/tmp/tmpqkd9zdgq/files/6/a/0/dataset_6a00d93a-ee34-42d5-897b-9470d6c71e1f.dat" ext="bam" label="merlin-sample.bam">
                <metadata>
                  <dataset id="adba32ec9811aba7" hid="2"
                      size="12.9 KB"
                      edam_format="format_2572"
                      file_ext="bam" />
                  <history id="a90a30fafe298e1e"
                      user_email="[e-mail]"
                      user_id="2"
                      display_name="test_history"/>
                  <metadata
                      dbkey="?"
                      bam_version="1.3"
                      sort_order="coordinate"
                      reference_names="[SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7f3deb10ba10 on: u__sq__Merlin__sq__]"
                      reference_lengths="[172788]"
                      columns="12"
                      bam_index="__lt__galaxy.model.MetadataFile(1) at 0x7f3de95da7d0__gt__"
                      />
                  <tool
                      tool_id="upload1"
                      tool_version="1.1.6"
                      />
                </metadata>
              </trackFile>
            </files>

            <options>
                <custom_config>
                </custom_config>

                <pileup>
                    <auto_snp>false</auto_snp>
                    <bam_indices>
                        <bam_index>/tmp/tmpqkd9zdgq/files/_metadata_files/a/5/2/metadata_a520581b-e8cc-43e5-8514-3379cd5eaafb.dat</bam_index>
                    </bam_indices>
                    <chunkSizeLimit>5000000</chunkSizeLimit>
                </pileup>
            </options>
        </track>
    </tracks>
    <plugins
        ComboTrackSelector=""
        Bookmarks=""
        GCContent=""
        BlastView="True"
        theme=""
        />
</root>