view x/galaxy.xml @ 133:cec274db51c0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7d28252954cae9f8db5f8a85d8f29cb2865b504b-dirty
author fubar
date Fri, 18 Oct 2024 11:57:55 +0000
parents fbabf7498471
children
line wrap: on
line source

<?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>

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                          edam_format="format_1929"
                          file_ext="fasta"
                          dname = "Merlin"
                          />
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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="2881"
                              sequences="1"
                          />
                      <tool
                          tool_id="upload1"
                          tool_version="1.1.7"
                          />
                    </metadata>
                  </genome>
            </genomes>
    </metadata>
    <tracks>
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                    <files>
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                                  <dataset id="f899122287bdd0b2" hid="2"
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                                      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">
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                                      file_ext="bigwig" />
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                                      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>
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                                      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="?"
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                                        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">
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                                  <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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                                        column_names="[]"
                                        delimiter="__tc__"
                                        viz_filter_cols="[5]"
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                                      />
                                  <tool
                                      tool_id="upload1"
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                                      />
                                </metadata>
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                      <options>
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                                    <trackShowDescriptions>false</trackShowDescriptions>
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                    <files>
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                                      display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
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                                        cram_version="3.0"
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                                  <tool
                                      tool_id="upload1"
                                      tool_version="1.1.7"
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                                </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,
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                            </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">
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                                      display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
                                  <metadata
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                                        column_names="[QNAME,FLAG,RNAME,POS,MAPQ,CIGAR,MRNM,MPOS,ISIZE,SEQ,QUAL,OPT]"
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                                        sort_order="coordinate"
                                        read_groups="[]"
                                        reference_names="[Merlin]"
                                        reference_lengths="[172788]"
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                                  <tool
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                                      tool_version="1.1.7"
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                      <options>
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                            </bam>
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                    <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">
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                                  <history id="801225f8dc4ca2f7"
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                                      display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
                                  <metadata
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                                        data_lines="0"
                                        species="[Merlin,Merlin1,Merlin2,Merlin3,Merlin4,Merlin5,Merlin6]"
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                                  <tool
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                    </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">
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                                  <tool
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                                </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>
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                              </trackFile>
                    </files>
                      <options>
                        <style>
                                <type>LinearAlignmentsDisplay</type>
                        </style>
                            <bam>
                            <bam_index>
                                    /tmp/tmpus622kw5/files/c/d/9/dataset_cd94dba1-9bb2-4c84-ba3b-a9b269faf031.dat ~ ,
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                            </bam>
                        </options>
                  </track>
    </tracks>
    </assembly>
    <assembly>
        <metadata>
            <genomes>
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                      <history
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                          display_name="Tool Test History for jbrowse2/2.15.4+galaxy2-0"/>
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                      <metadata
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                              sequences="1"
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                      <tool
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                          />
                    </metadata>
                  </genome>
            </genomes>
    </metadata>
    <tracks>
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                              <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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                                  <tool
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                      <options>
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                                <type>LinearHicDisplay</type>
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                            <cool>
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    </assembly>
    <assembly>
        <metadata>
            <genomes>
                  <genome path="/tmp/tmpus622kw5/files/a/d/d/dataset_add7c5ef-1f3d-4c73-9d9c-43892361ebfe.dat" label="Ppersica1.fa" useuri="no">
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                      <metadata
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                              sequences="1"
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                      <tool
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                          tool_version="1.1.7"
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                    </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">
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                                  <tool
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                                </metadata>
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                      <options>
                        <style>
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                            <paf>
                                <genome>
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                                <useuri>
                                    false
                                </useuri>
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                    <track cat="Assembly properties" format="paf" visibility="default_on">
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                                </metadata>
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                      <options>
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                            <paf>
                                <genome>
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                                <useuri>
                                    true
                                </useuri>
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                                    false
                                </useuri>
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    </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>
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                            <hic>
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    </assembly>
</root>