Mercurial > repos > iuc > jbrowse2
diff test-data/out/02_remote/galaxy.xml @ 0:61add3f58f26 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
| author | iuc |
|---|---|
| date | Thu, 02 Oct 2025 10:19:44 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out/02_remote/galaxy.xml Thu Oct 02 10:19:44 2025 +0000 @@ -0,0 +1,257 @@ +<?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>