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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5903fd8076687ad01a7cf0a522b954106ac6579a
author fubar
date Wed, 24 Apr 2024 03:25:23 +0000
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<?xml version="1.0"?>
<root>
    <metadata>
        <general>
            <defaultLocation></defaultLocation>
            <zipOut>true</zipOut>
            <analytics>false</analytics>
            <primary_color>#0d233f</primary_color>
            <secondary_color>#721e63</secondary_color>
            <tertiary_color>#135560</tertiary_color>
            <quaternary_color>#ffb11d</quaternary_color>
            <font_size>10</font_size>
            <session_name>New test session</session_name>
        </general>
        <galaxyUrl>http://localhost:8080</galaxyUrl>
    </metadata>
    <assembly>
        <metadata>
            <genomes>
                  <genome path="/tmp/tmpaivwlly7/files/2/6/5/dataset_265ba9ba-75c3-49ca-be12-7c34a7b56380.dat" label="Merlin" useuri="no">
                    <metadata>

                      <dataset id="e3f2f10afcaf3f83"
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                          size="171.6 KB"
                          edam_format="format_1929"
                          file_ext="fasta"
                          dname = "Merlin"
                          />
                      <history
                          user_email="planemo@galaxyproject.org"
                          user_id="1"
                          display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>
                          id="e3f2f10afcaf3f83"
                          />
                      <metadata
                              dbkey="?"
                              data_lines="2881"
                              sequences="1"
                          />
                      <tool
                          tool_id="upload1"
                          tool_version="1.1.7"
                          />

                    </metadata>
                  </genome>
            </genomes>
    </metadata>
    <tracks>
                    <track cat="Assembly properties" format="gff" visibility="default_on">
                    <files>
                              <trackFile path="/tmp/tmpaivwlly7/files/8/d/6/dataset_8d6c2542-1af4-4bd1-ab96-98e31f60a542.dat" ext="gff3" label="merlin.gff3" useuri="no">
                                <metadata>

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                                      file_ext="gff3" />
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                                      user_id="1"
                                      display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>

                                  <metadata
                                        dbkey="?"
                                        data_lines="9"
                                        comment_lines="10"
                                        columns="9"
                                        column_names="[]"
                                        delimiter="__tc__"
                                        attributes="23"
                                      />
                                  <tool
                                      tool_id="upload1"
                                      tool_version="1.1.7"
                                      />
                                </metadata>
                              </trackFile>
                    </files>
                      <options>
                        <style>
                                <type>LinearBasicDisplay</type>
                                    <trackShowLabels>false</trackShowLabels>
                                    <trackShowDescriptions>false</trackShowDescriptions>
                        </style>
                            <gff>
                            </gff>
                        </options>
                  </track>
                    <track cat="Assembly properties" format="bigwig" visibility="default_on">
                    <files>
                              <trackFile path="/tmp/tmpaivwlly7/files/b/e/0/dataset_be0fc51e-5417-47ca-bfd0-6bc92397dbd5.dat" ext="bigwig" label="merlin.bw" useuri="no">
                                <metadata>

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                                      file_ext="bigwig" />
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                                      user_id="1"
                                      display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>

                                  <metadata
                                        dbkey="?"
                                      />
                                  <tool
                                      tool_id="upload1"
                                      tool_version="1.1.7"
                                      />
                                </metadata>
                              </trackFile>
                    </files>
                      <options>
                        <style>
                        </style>
                        </options>
                  </track>
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                    <files>
                              <trackFile path="/tmp/tmpaivwlly7/files/7/3/c/dataset_73c83085-225b-4587-ac6d-84b74ab74412.dat" ext="bed" label="test-6.bed" useuri="no">
                                <metadata>

                                  <dataset id="482da5c8895b0100" hid="4"
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                                      file_ext="bed" />
                                  <history id="e3f2f10afcaf3f83"
                                      user_email="planemo@galaxyproject.org"
                                      user_id="1"
                                      display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>

                                  <metadata
                                        dbkey="?"
                                        data_lines="3"
                                        comment_lines="0"
                                        columns="6"
                                        column_names="[]"
                                        delimiter="__tc__"
                                        chromCol="1"
                                        startCol="2"
                                        endCol="3"
                                        strandCol="6"
                                        viz_filter_cols="[4]"
                                      />
                                  <tool
                                      tool_id="upload1"
                                      tool_version="1.1.7"
                                      />
                                </metadata>
                              </trackFile>
                    </files>
                      <options>
                        <style>
                                <type>LinearBasicDisplay</type>
                                    <trackShowLabels>false</trackShowLabels>
                                    <trackShowDescriptions>false</trackShowDescriptions>
                        </style>
                            <bed>
                            </bed>
                        </options>
                  </track>
                    <track cat="Assembly properties" format="vcf" visibility="default_on">
                    <files>
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                                <metadata>

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                                      file_ext="vcf" />
                                  <history id="e3f2f10afcaf3f83"
                                      user_email="planemo@galaxyproject.org"
                                      user_id="1"
                                      display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>

                                  <metadata
                                        dbkey="?"
                                        data_lines="5"
                                        comment_lines="18"
                                        columns="12"
                                        column_names="[]"
                                        delimiter="__tc__"
                                        viz_filter_cols="[5]"
                                        sample_names="[NA00001,NA00002,NA00003]"
                                      />
                                  <tool
                                      tool_id="upload1"
                                      tool_version="1.1.7"
                                      />
                                </metadata>
                              </trackFile>
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                      <options>
                        <style>
                                <type>LinearVariantDisplay</type>
                                    <trackShowLabels>false</trackShowLabels>
                                    <trackShowDescriptions>false</trackShowDescriptions>

                        </style>
                        </options>
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                                <metadata>

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                                      user_id="1"
                                      display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>

                                  <metadata
                                        dbkey="?"
                                        cram_version="3.0"
                                        cram_index="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
                                      />
                                  <tool
                                      tool_id="upload1"
                                      tool_version="1.1.7"
                                      />
                                </metadata>
                              </trackFile>
                    </files>
                      <options>
                        <style>
                                <type>LinearAlignmentsDisplay</type>
                        </style>
                            <cram>
                            <cram_index>
                                    /tmp/tmpaivwlly7/files/6/b/d/dataset_6bd63ebf-abbf-4225-b2a9-50021936ba0b.dat:/tmp/tmpaivwlly7/files/_metadata_files/6/d/8/metadata_6d808e2c-4839-4fbd-be66-dddc3e317c0e.dat,
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                            </cram>
                        </options>
                  </track>
                    <track cat="Assembly properties" format="bam" visibility="default_on">
                    <files>
                              <trackFile path="/tmp/tmpaivwlly7/files/7/5/8/dataset_758f55d0-ac29-4407-9708-0574143d9156.dat" ext="bam" label="merlin-sample.bam" useuri="no">
                                <metadata>

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                                      display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>

                                  <metadata
                                        dbkey="?"
                                        columns="12"
                                        column_names="[QNAME,FLAG,RNAME,POS,MAPQ,CIGAR,MRNM,MPOS,ISIZE,SEQ,QUAL,OPT]"
                                        bam_version="1.3"
                                        sort_order="coordinate"
                                        read_groups="[]"
                                        reference_names="[Merlin]"
                                        reference_lengths="[172788]"
                                        bam_index="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
                                      />
                                  <tool
                                      tool_id="upload1"
                                      tool_version="1.1.7"
                                      />
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                    </files>
                      <options>
                        <style>
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                            <bam>
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                                    /tmp/tmpaivwlly7/files/7/5/8/dataset_758f55d0-ac29-4407-9708-0574143d9156.dat:/tmp/tmpaivwlly7/files/_metadata_files/f/f/f/metadata_fff68af6-01d7-40db-a788-ee6938456d5f.dat,
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                                <metadata>

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                                      file_ext="maf" />
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                                      display_name="Tool Test History for jbrowse2/2.10.1+galaxy2_15-0"/>

                                  <metadata
                                        dbkey="?"
                                        data_lines="0"
                                        species="[Merlin,Merlin1,Merlin2,Merlin3,Merlin4,Merlin5,Merlin6]"
                                        blocks="6"
                                        species_chromosomes="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
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                                      />
                                  <tool
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                                      />
                                </metadata>
                              </trackFile>
                    </files>
                      <options>
                        <style>
                                <type>LinearBasicDisplay</type>
                                    <trackShowLabels>false</trackShowLabels>
                                    <trackShowDescriptions>false</trackShowDescriptions>
                        </style>
                        </options>
                  </track>
                    <track cat="Assembly properties" format="blastxml" visibility="default_on">
                    <files>
                              <trackFile path="/tmp/tmpaivwlly7/files/f/e/0/dataset_fe0756a4-6131-49ae-9ee8-75fda299d112.dat" ext="blastxml" label="merlin.blastxml" useuri="no">
                                <metadata>

                                  <dataset id="cc3513adc598b906" hid="9"
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                                  <metadata
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                                      />
                                  <tool
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                                      />
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                              </trackFile>
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                      <options>
                        <style>
                                <type>LinearBasicDisplay</type>
                                    <trackShowLabels>false</trackShowLabels>
                                    <trackShowDescriptions>false</trackShowDescriptions>
                        </style>
                            <blast>
                                <parent>None</parent>
                                <protein>false</protein>
                                <min_gap>10</min_gap>
                            </blast>
                        </options>
                  </track>
                    <track cat="Assembly properties" format="bam" visibility="default_on">
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                                  <metadata
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                      <tool
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                          />

                    </metadata>
                  </genome>
            </genomes>
    </metadata>
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                    </metadata>
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    </assembly>
</root>