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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 3cf9ec268c0719caf060b7d6bf5c0159909c348a
author fubar
date Sat, 12 Oct 2024 23:11:22 +0000
parents fbabf7498471
children
line wrap: on
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<?xml version="1.0"?>
<root>
    <metadata>
        <general>
            <defaultLocation></defaultLocation>
            <zipOut>true</zipOut>
            <bpPerPx>50</bpPerPx>
            <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/tmpus622kw5/files/7/4/8/dataset_748d2461-ea0f-4e92-b129-e680b76d4c81.dat" label="Merlin" useuri="no">
                    <metadata>

                      <dataset id="801225f8dc4ca2f7"
                          hid="1"
                          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 jbrowse2/2.15.4+galaxy2-0"/>
                          id="801225f8dc4ca2f7"
                          />
                      <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/tmpus622kw5/files/b/7/d/dataset_b7de2a4d-8123-493d-99ad-6f251912ae1c.dat" ext="gff3" label="merlin.gff3" useuri="no">
                                <metadata>
                                  <dataset id="f899122287bdd0b2" hid="2"
                                      size="5.0 KB"
                                      edam_format="format_1975"
                                      file_ext="gff3" />
                                  <history id="801225f8dc4ca2f7"
                                      user_email="planemo@galaxyproject.org"
                                      user_id="1"
                                      display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
                                  <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/tmpus622kw5/files/b/5/2/dataset_b523b4bc-c4b6-4eb0-a914-364fb4f91db4.dat" ext="bigwig" label="merlin.bw" useuri="no">
                                <metadata>
                                  <dataset id="78cc944b7b4634f8" hid="3"
                                      size="81.6 KB"
                                      edam_format="format_3006"
                                      file_ext="bigwig" />
                                  <history id="801225f8dc4ca2f7"
                                      user_email="planemo@galaxyproject.org"
                                      user_id="1"
                                      display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
                                  <metadata
                                        dbkey="?"
                                      />
                                  <tool
                                      tool_id="upload1"
                                      tool_version="1.1.7"
                                      />
                                </metadata>
                              </trackFile>
                    </files>
                      <options>
                        <style>
                                <type>LinearWiggleDisplay</type>
                                <color>#135560</color>
                                <autoscale>globalsd</autoscale>
                                <resolution>1</resolution>
                                <summaryScoreMode>whiskers</summaryScoreMode>
                                <filled>true</filled>
                                <scaleType>linear</scaleType>
                                <displayCrossHatches>true</displayCrossHatches>
                                <minScore></minScore>
                                <maxScore></maxScore>
                        </style>
                        </options>
                  </track>
                    <track cat="Assembly properties" format="bed" visibility="default_on">
                    <files>
                              <trackFile path="/tmp/tmpus622kw5/files/b/1/3/dataset_b132250a-57b0-4f00-a94b-be3b7b14fa98.dat" ext="bed" label="test-6.bed" useuri="no">
                                <metadata>
                                  <dataset id="3628324a9a091ab7" hid="4"
                                      size="180 bytes"
                                      edam_format="format_3003"
                                      file_ext="bed" />
                                  <history id="801225f8dc4ca2f7"
                                      user_email="planemo@galaxyproject.org"
                                      user_id="1"
                                      display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
                                  <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>
                                <usebedscore>false</usebedscore>
                            </bed>
                        </options>
                  </track>
                    <track cat="Assembly properties" format="vcf" visibility="default_on">
                    <files>
                              <trackFile path="/tmp/tmpus622kw5/files/4/9/6/dataset_49609184-5279-4c15-8e1a-b492552a02ff.dat" ext="vcf" label="merlin.vcf" useuri="no">
                                <metadata>
                                  <dataset id="7e78e1a21bf444fa" hid="5"
                                      size="1.5 KB"
                                      edam_format="format_3016"
                                      file_ext="vcf" />
                                  <history id="801225f8dc4ca2f7"
                                      user_email="planemo@galaxyproject.org"
                                      user_id="1"
                                      display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
                                  <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>
                    </files>
                      <options>
                        <style>
                                <type>LinearVariantDisplay</type>
                                    <trackShowLabels>false</trackShowLabels>
                                    <trackShowDescriptions>false</trackShowDescriptions>
                        </style>
                        </options>
                  </track>
                    <track cat="Assembly properties" format="cram" visibility="default_on">
                    <files>
                              <trackFile path="/tmp/tmpus622kw5/files/8/6/5/dataset_86597dfb-d461-4ef9-9eb6-c8262351f18c.dat" ext="cram" label="merlin.cram" useuri="no">
                                <metadata>
                                  <dataset id="80ac834e53a3892f" hid="6"
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                                      edam_format="format_3462"
                                      file_ext="cram" />
                                  <history id="801225f8dc4ca2f7"
                                      user_email="planemo@galaxyproject.org"
                                      user_id="1"
                                      display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
                                  <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/tmpus622kw5/files/8/6/5/dataset_86597dfb-d461-4ef9-9eb6-c8262351f18c.dat ~ /tmp/tmpus622kw5/files/_metadata_files/c/d/8/metadata_cd855eb8-90c3-478b-af5d-47ba048c1765.dat,
                            </cram_index>
                            </cram>
                        </options>
                  </track>
                    <track cat="Assembly properties" format="bam" visibility="default_on">
                    <files>
                              <trackFile path="/tmp/tmpus622kw5/files/d/6/8/dataset_d6878dfb-6c11-4673-a348-d7c441e5c7db.dat" ext="bam" label="merlin-sample.bam" useuri="no">
                                <metadata>
                                  <dataset id="64ba8fadcb1fc688" hid="7"
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                                      edam_format="format_2572"
                                      file_ext="bam" />
                                  <history id="801225f8dc4ca2f7"
                                      user_email="planemo@galaxyproject.org"
                                      user_id="1"
                                      display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
                                  <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"
                                      />
                                </metadata>
                              </trackFile>
                    </files>
                      <options>
                        <style>
                                <type>LinearAlignmentsDisplay</type>
                        </style>
                            <bam>
                            <bam_index>
                                    /tmp/tmpus622kw5/files/d/6/8/dataset_d6878dfb-6c11-4673-a348-d7c441e5c7db.dat ~ /tmp/tmpus622kw5/files/_metadata_files/8/9/f/metadata_89f41037-55f2-4252-9884-5eba8bd4e748.dat,
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                            </bam>
                        </options>
                  </track>
                    <track cat="Assembly properties" format="maf" visibility="default_on">
                    <files>
                              <trackFile path="/tmp/tmpus622kw5/files/f/e/c/dataset_feca1abe-d55a-4ade-a506-1e1f99e76cb3.dat" ext="maf" label="merlinlastz.maf" useuri="no">
                                <metadata>
                                  <dataset id="d64497191f3f5d7f" hid="8"
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                                      edam_format="format_3008"
                                      file_ext="maf" />
                                  <history id="801225f8dc4ca2f7"
                                      user_email="planemo@galaxyproject.org"
                                      user_id="1"
                                      display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
                                  <metadata
                                        dbkey="?"
                                        data_lines="0"
                                        species="[Merlin,Merlin1,Merlin2,Merlin3,Merlin4,Merlin5,Merlin6]"
                                        blocks="6"
                                        species_chromosomes="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
                                        maf_index="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
                                      />
                                  <tool
                                      tool_id="upload1"
                                      tool_version="1.1.7"
                                      />
                                </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/tmpus622kw5/files/3/6/5/dataset_365aaf8d-17be-44d6-93c7-dc4952ef511b.dat" ext="blastxml" label="merlin.blastxml" useuri="no">
                                <metadata>
                                  <dataset id="3a8027169fd7c75d" hid="9"
                                      size="1.6 MB"
                                      edam_format="format_3331"
                                      file_ext="blastxml" />
                                  <history id="801225f8dc4ca2f7"
                                      user_email="planemo@galaxyproject.org"
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                                      display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
                                  <metadata
                                        dbkey="?"
                                        data_lines="20455"
                                      />
                                  <tool
                                      tool_id="upload1"
                                      tool_version="1.1.7"
                                      />
                                </metadata>
                              </trackFile>
                    </files>
                      <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">
                    <files>
                              <trackFile path="/tmp/tmpus622kw5/files/c/d/9/dataset_cd94dba1-9bb2-4c84-ba3b-a9b269faf031.dat" ext="zip" label="files_0Xfile_data" useuri="no">
                                <metadata>
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                                      size="275.3 KB"
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                                      file_ext="zip" />
                                  <history id="801225f8dc4ca2f7"
                                      user_email="planemo@galaxyproject.org"
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                                      display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
                                  <metadata
                                        dbkey="?"
                                      />
                                  <tool
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                                      tool_version="1.1.7"
                                      />
                                </metadata>
                              </trackFile>
                    </files>
                      <options>
                        <style>
                                <type>LinearAlignmentsDisplay</type>
                        </style>
                            <bam>
                            <bam_index>
                                    /tmp/tmpus622kw5/files/c/d/9/dataset_cd94dba1-9bb2-4c84-ba3b-a9b269faf031.dat ~ ,
                            </bam_index>
                            </bam>
                        </options>
                  </track>
    </tracks>
    </assembly>
    <assembly>
        <metadata>
            <genomes>
                  <genome path="/tmp/tmpus622kw5/files/a/e/2/dataset_ae2fbecc-5b2d-4783-9ff9-dc4c0827a344.dat" label="dm3.fa" useuri="no">
                    <metadata>

                      <dataset id="47bf7b7c957123a5"
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                          size="27.2 MB"
                          edam_format="format_1929"
                          file_ext="fasta"
                          dname = "dm3.fa"
                          />
                      <history
                          user_email="planemo@galaxyproject.org"
                          user_id="1"
                          display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
                          id="801225f8dc4ca2f7"
                          />
                      <metadata
                              dbkey="?"
                              data_lines="401577"
                              sequences="1"
                          />
                      <tool
                          tool_id="upload1"
                          tool_version="1.1.7"
                          />
                    </metadata>
                  </genome>
            </genomes>
    </metadata>
    <tracks>
                    <track cat="Assembly properties" format="cool" visibility="default_on">
                    <files>
                              <trackFile path="/tmp/tmpus622kw5/files/5/2/8/dataset_528eb872-92fa-4d06-bda9-b8c3522f6b50.dat" ext="cool" label="dm3test.cool" useuri="no">
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                                      file_ext="cool" />
                                  <history id="801225f8dc4ca2f7"
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                                      display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
                                  <metadata
                                        dbkey="?"
                                      />
                                  <tool
                                      tool_id="upload1"
                                      tool_version="1.1.7"
                                      />
                                </metadata>
                              </trackFile>
                    </files>
                      <options>
                        <style>
                                <type>LinearHicDisplay</type>
                        </style>
                            <cool>
                            </cool>
                        </options>
                  </track>
    </tracks>
    </assembly>
    <assembly>
        <metadata>
            <genomes>
                  <genome path="/tmp/tmpus622kw5/files/a/d/d/dataset_add7c5ef-1f3d-4c73-9d9c-43892361ebfe.dat" label="Ppersica1.fa" useuri="no">
                    <metadata>

                      <dataset id="1cd311606732130f"
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                          file_ext="fasta"
                          dname = "Ppersica1.fa"
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                      <history
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                          user_id="1"
                          display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
                          id="801225f8dc4ca2f7"
                          />
                      <metadata
                              dbkey="?"
                              data_lines="598142"
                              sequences="1"
                          />
                      <tool
                          tool_id="upload1"
                          tool_version="1.1.7"
                          />
                    </metadata>
                  </genome>
            </genomes>
    </metadata>
    <tracks>
                    <track cat="Assembly properties" format="paf" visibility="default_on">
                    <files>
                              <trackFile path="/tmp/tmpus622kw5/files/3/9/6/dataset_396ed6d5-d81e-4a2e-b566-1b69cf0a8ec0.dat" ext="paf" label="peach-grape-map.paf" useuri="no">
                                <metadata>
                                  <dataset id="4a3497682f135c57" hid="14"
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                                      edam_format="format_2330"
                                      file_ext="paf" />
                                  <history id="801225f8dc4ca2f7"
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                                      user_id="1"
                                      display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
                                  <metadata
                                        dbkey="?"
                                        data_lines="9291"
                                      />
                                  <tool
                                      tool_id="upload1"
                                      tool_version="1.1.7"
                                      />
                                </metadata>
                              </trackFile>
                    </files>
                      <options>
                        <style>
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                            <paf>
                                <genome>
                                        /tmp/tmpus622kw5/files/e/4/4/dataset_e44ca09b-d9ff-4a99-a4cb-e50f24a66ff9.dat ~ Vvinifera1.fa,
                                </genome>
                                <useuri>
                                    false
                                </useuri>
                            </paf>
                        </options>
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                    <track cat="Assembly properties" format="paf" visibility="default_on">
                    <files>
                              <trackFile path="/tmp/tmpus622kw5/files/2/7/2/dataset_272188a9-0367-4677-9b28-ad5e84aceb99.dat" ext="paf" label="arabgrapepeach.paf" useuri="no">
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                                      display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
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                                  <tool
                                      tool_id="upload1"
                                      tool_version="1.1.7"
                                      />
                                </metadata>
                              </trackFile>
                    </files>
                      <options>
                        <style>
                        </style>
                            <paf>
                                <genome>
                                        https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa.gz ~ arabidopsis.URI,
                                        https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz ~ Vvinifera1.URI,
                                </genome>
                                <useuri>
                                    true
                                </useuri>
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                    <track cat="Assembly properties" format="paf" visibility="default_on">
                    <files>
                              <trackFile path="/tmp/tmpus622kw5/files/2/7/2/dataset_272188a9-0367-4677-9b28-ad5e84aceb99.dat" ext="paf" label="arabgrapepeach.paf" useuri="no">
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                                      file_ext="paf" />
                                  <history id="801225f8dc4ca2f7"
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                                      user_id="1"
                                      display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
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                                      />
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                                      tool_version="1.1.7"
                                      />
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                      <options>
                        <style>
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                            <paf>
                                <genome>
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                                </genome>
                                <useuri>
                                    false
                                </useuri>
                            </paf>
                        </options>
                  </track>
    </tracks>
    </assembly>
    <assembly>
        <metadata>
            <genomes>
                  <genome path="https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz" label="hg38" useuri="yes">
                      <metadata>
                         <dataset
                          dname = "hg38" />
                  </metadata>
                  </genome>
            </genomes>
    </metadata>
    <tracks>
                        <track cat="Assembly properties" format="hic" visibility="default_on">
                            <files>
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                                    label="humanhic" useuri="yes">
                                    <metadata>
                                    <dataset id = "https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic" />
                                    </metadata>
                                 </trackFile>
                            </files>
                      <options>
                        <style>
                                <type>LinearHicDisplay</type>
                        </style>
                            <hic>
                            </hic>
                        </options>
                  </track>
    </tracks>
    </assembly>
</root>