annotate test-data/out/02_remote/galaxy.xml @ 138:bd903fbbc26e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse2 commit c69a3ef64924b2b66862818675cb9bde66499ed6

<?xml version="1.0"?>
<root>
    <metadata>
        <general>
            <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>
        </general>
        <galaxyUrl>http://localhost:8080</galaxyUrl>
    </metadata>
    <assembly>
            <genome path="https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz" label="hg19" remote="true">
                <metadata />
            </genome>
        <defaultLocation></defaultLocation>
    <tracks>
        <track cat="Default" format="wiggle" visibility="default_on">


                    <files>
                    <trackFile path="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw" ext="bigwig" label="SKBR3 pacbio coverage (NGMLR)" remote="true">
                        <metadata>
                        </metadata>
                    </trackFile>
                    </files>

            <options>
                <style>
                        <display>LinearWiggleDisplay</display>



                        <renderer>xyplot</renderer>
                </style>



                    <wiggle>
                    </wiggle>
            </options>
        </track>
        <track cat="Default" format="wiggle" visibility="default_on">


                    <files>
                    <trackFile path="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw" ext="bigwig" label="SKBR3 pacbio coverage (NGMLR)" remote="true">
                        <metadata>
                        </metadata>
                    </trackFile>
                    </files>

            <options>
                <style>
                        <display>MultiLinearWiggleDisplay</display>



                        <renderer>multirowxy</renderer>
                </style>


                        <multitrack type="boolean">True</multitrack>

                    <wiggle>
                    </wiggle>
            </options>
        </track>
        <track cat="Default" format="pileup" visibility="default_on">


                    <files>
                    <trackFile path="https://s3.amazonaws.com/1000genomes/phase3/data/NA12878/exome_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam" ext="bam" label="NA12878 Exome" remote="true">
                        <metadata>
                        </metadata>
                    </trackFile>
                    </files>

            <options>
                <style>
                        <display>LinearAlignmentsDisplay</display>



                </style>



                    <pileup>
                    </pileup>
            </options>
        </track>
        <track cat="Default" format="cram" visibility="default_on">


                    <files>
                    <trackFile path="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/alzheimers_isoseq/hq_isoforms.fasta.cram" ext="cram" label="hg_isoforms.fasta_cram" remote="true">
                        <metadata>
                        </metadata>
                    </trackFile>
                    </files>

            <options>
                <style>
                        <display>LinearAlignmentsDisplay</display>



                </style>



                    <cram>
                    </cram>
            </options>
        </track>
        <track cat="Default" format="hic" visibility="default_on">


                    <files>
                    <trackFile path="https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic" ext="hic" label="hg_isoforms.fasta_cram" remote="true">
                        <metadata>
                        </metadata>
                    </trackFile>
                    </files>

            <options>
                <style>
                        <display>LinearHicDisplay</display>



                </style>



                    <hic>
                    </hic>
            </options>
        </track>
        <track cat="Default" format="vcf" visibility="default_on">


                    <files>
                    <trackFile path="https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/vcf/nstd175.GRCh37.variant_call.vcf.gz" ext="vcf,vcf_bgzip" label="HG002 dbVar variant calls" remote="true">
                        <metadata>
                        </metadata>
                    </trackFile>
                    </files>

            <options>
                <style>
                        <display>LinearVariantDisplay</display>



                </style>



            </options>
        </track>
        <track cat="Default" format="vcf" visibility="default_on">


                    <files>
                    <trackFile path="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/COLO829/truthset_somaticSVs_COLO829.vcf" ext="vcf,vcf_bgzip" label="truthset_somaticSVs_COLO829" remote="true">
                        <metadata>
                        </metadata>
                    </trackFile>
                    </files>

            <options>
                <style>
                        <display>LinearVariantDisplay</display>



                </style>



            </options>
        </track>
        <track cat="Default" format="gene_calls" visibility="default_on">


                    <files>
                    <trackFile path="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gencode/gencode.v36lift37.annotation.sort.gff3.gz" ext="gff,gff3,bed" label="Gencode v36 (GRCh37 liftover)" remote="true">
                        <metadata>
                        </metadata>
                    </trackFile>
                    </files>

            <options>
                <style>
                        <display>LinearBasicDisplay</display>

                            <show_labels type="boolean">true</show_labels>
                            <show_descriptions type="boolean">true</show_descriptions>
                            <labels_name>jexl:get(feature,'name') || get(feature,'id')</labels_name>
                            <descriptions_name>jexl:get(feature,'note') || get(feature,'description')</descriptions_name>
                            <display_mode>normal</display_mode>
                            <max_height type="integer">600</max_height>


                </style>

                    <formatdetails>
                        <depth>1</depth>
                    </formatdetails>


                    <gff>
                    <index>false</index>
                    </gff>
            </options>
        </track>
        <track cat="Default" format="gene_calls" visibility="default_on">


                    <files>
                    <trackFile path="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/mappability/wgEncodeDukeMapabilityRegionsExcludable.bed.gz" ext="gff,gff3,bed" label="wgEncodeDukeMapabilityRegionsExcludable" remote="true">
                        <metadata>
                        </metadata>
                    </trackFile>
                    </files>

            <options>
                <style>
                        <display>LinearBasicDisplay</display>

                            <show_labels type="boolean">true</show_labels>
                            <show_descriptions type="boolean">true</show_descriptions>
                            <labels_name>jexl:get(feature,'name') || get(feature,'id')</labels_name>
                            <descriptions_name>jexl:get(feature,'note') || get(feature,'description')</descriptions_name>
                            <display_mode>normal</display_mode>
                            <max_height type="integer">600</max_height>


                </style>

                    <formatdetails>
                        <depth>1</depth>
                    </formatdetails>


                    <gff>
                    <index>false</index>
                    </gff>
            </options>
        </track>
    </tracks>
    </assembly>
</root>