track cpgIslandSuperTrack
type bigBed
shortLabel cpgIsland SuperTrack Container
longLabel cpgIsland SuperTrack Container
superTrack on

    track cpgIslandExt_
    type bigBed 4 +
    parent cpgIslandSuperTrack
    longLabel CpG Islands (Islands < 300 Bases are Light Green)
    color 0,100,0
    altColor 128,228,128
    bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.cpgIslandExt.bb
    priority 90
    html http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/trackDescriptions/cpgIslandExt
    group regulation
    shortLabel CpG Islands
    visibility pack

#track cpgIslandIncorrect
#type bigBed
#shortLabel trackWithNoParent
#longLabel trackWithNoParent
#bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.cpgIslandExt.bb
#parent missingParent

track cpgIslandViewContainer
compositeTrack on
shortLabel trackWithViewContainer
longLabel trackWithViewContainer
subGroup1 view Views A=a
type bed

    track viewStanza
    parent cpgIslandViewContainer
    shortLabel viewStanza
    longLabel viewStanza
    view a
    type bigBed
        
        track viewTrack
        shortLabel viewTrack
        longLabel viewTrack
        bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.cpgIslandExt.bb
        subGroups A=a
        parent viewStanza
        type bigBed

#track cpgIslandWrongParent
#type bigBed
#shortLabel trackWrongParent
#longLabel trackWrongParent
#bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.cpgIslandExt.bb

    #track cpgIslandBadChild
    #type bigBed
    #shortLabel trackWithWrongParent
    #longLabel trackWithWrongParent
    #bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.cpgIslandExt.bb
    #parent cpgIslandWrongParent

track repeatMasker_
noInherit on
type bed 6 .
longLabel Repeating Elements by RepeatMasker
priority 149.1
compositeTrack on
html http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/trackDescriptions/repeatMasker
group varRep
shortLabel RepeatMasker
#correct:
#subGroup1 view Views SuperEnhancers=ROSE
#dimensions dimX=view
#sortOrder view=+
#incorrect:
subGroup1 source Source EnsRegBuild=Regulatory_Build TFBS=Transcription_Factor_Binding_Site_Peaks_Summary
subGroup2 blank Blank Tag1=Val1
#dimensions dimY=source 
sortOrder source=+
visibility dense

    track repeatMaskerSINE_
    #correct:
    #subGroups view=SuperEnhancers
    #incorrect:
    subGroups source=EnsRegBuild noGroup=badGroup
    type bigBed 6 +
    longLabel SINE Repeating Elements by RepeatMasker
    parent repeatMasker_
    bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.rmsk.SINE.bb
    priority 1
    maxWindowToDraw 10000000
    spectrum on
    shortLabel SINE
    colorByStrand 50,50,150 150,50,50

    track repeatMaskerSINE2
    #correct:
    #subGroups view=SuperEnhancers
    #incorrect:
    subGroups source=TFBS
    type bigBed 6 +
    longLabel SINE2 Repeating Elements by RepeatMasker
    parent repeatMasker_
    bigDataUrl http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.rmsk.SINE.bb
    priority 1
    maxWindowToDraw 10000000
    spectrum on
    shortLabel SINE2
    colorByStrand 50,50,150 150,50,50

#track emptyContainer
#compositeTrack on
#shortLabel missingChildren
#longLabel missingChildren
#type bigWig

track SuperEnhancersBadSubgroups
superTrack on
shortLabel SuperenhancersBadSubgroups
longLabel Superenhancers

    track SuperEnhancersBadSubgroupsComposite
    compositeTrack on
    #bigDataUrl http://should.not.have/one.bb
    parent SuperEnhancersBadSubgroups
    shortLabel SuperEnhancersBadSubgroupsComp
    longLabel SuperEnhancersBadSubgroupsComp
    subGroup1 view Views SuperEnhancers=ROSE
    dimensions dimensionX=view
    sortOrder view=+
    dividers view
    dragAndDrop on
    visibility dense
    type bigBed 3 +

        track state1
        shortLabel state1shortLabel
        longLabel state1LongLabel
        #subGroups view=SuperEnhancers
        view ROSE
        type bigBed 3 +
        visibility hide
        bigDataUrl http://genome-test.gi.ucsc.edu/~chmalee/hubValidate/plants/cshl2013/araTha1/CS13-12383_25state_dense_Gateway_SuperEnhancers.bigBed
        color 255,197,77
        parent SuperEnhancersBadSubgroupsComposite on

        track state2
        shortLabel state2shortLabel
        longLabel state2longLabel
        view ROSE
        #subGroups view=SuperEnhancers
        type bigBed 3 +
        visibility hide
        bigDataUrl  http://genome-test.gi.ucsc.edu/~chmalee/hubValidate/plants/cshl2013/araTha1/CS13-12690_25state_dense_Gateway_SuperEnhancers.bigBed
        color 255,197,77
        parent SuperEnhancersBadSubgroupsComposite on

track SuperEnhancersComposite2
compositeTrack on
#parent SuperEnhancersSuperTrackWithTwoSubgroups
shortLabel SuperEnhancersTwoSubsComp
longLabel SuperEnhancersTwoSubsComp
subGroup1 view Views SuperEnhancers=ROSE
subGroup2 tag Tags SuperEnhancers=ROSE
dimensions dimensionX=view dimensionY=tag
sortOrder view=+ tag=+
dividers view
dragAndDrop on
visibility dense
type bigBed 4 .
configurable on

    track state3
    configurable on
    shortLabel state3NoSubgroups
    longLabel state3NoSubgroups
    #subGroups view=SuperEnhancers tag=SuperEnhancers
    subGroups badTag=wrongName
    view ROSE
    type bigBed 4 .
    visibility hide
    bigDataUrl http://genome-test.gi.ucsc.edu/~chmalee/hubValidate/plants/cshl2013/araTha1/CS13-12383_25state_dense_Gateway_SuperEnhancers.bigBed
    color 255,197,77
    parent SuperEnhancersComposite2 on

    track state4
    shortLabel state4OneSubgroupMembership
    longLabel state4OneSubgorupMembership
    view ROSE
    subGroups view=SuperEnhancers
    type bigBed 4 .
    visibility hide
    bigDataUrl http://genome-test.gi.ucsc.edu/~chmalee/hubValidate/plants/cshl2013/araTha1/CS13-12690_25state_dense_Gateway_SuperEnhancers.bigBed
    color 255,197,77
    parent SuperEnhancersComposite2 on
    configurable on



track H2A.Z_MultiWig_ImputedComp
container multiWig
shortLabel H2A.Z_Summary
longLabel Summary Overlay for all Imputed H2A.Z Signal Tracks (21 Samples)
type bigWig

    track macs2signal_impute_CS13-12383_H2A.Z_M
    type bigWig
    shortLabel impute_CS13-12383_H2A.Z_M
    longLabel impute_CS13-12383_H2A.Z_M
    bigDataUrl https://bad.url.txt/missing.bb
    #bigDataUrl http://cotneylab.cam.uchc.edu/~jcotney/CRANIOFACIAL_HUB/hg19/impute_CS13-12383_H2A.Z.pval.signal.bigWig
    parent H2A.Z_MultiWig_ImputedComp on

track SuperTrackOfMultiWigsView
superTrack on
shortLabel supMultiWigView
longLabel supMultiWigView
#type bigBed

    track comp1
    compositeTrack on
    parent SuperTrackOfMultiWigsView
    subGroup1 view Views A=a B=b
    type bigWig
    shortLabel comp1
    longLabel comp1

        track comp1View1
        parent comp1
        shortLabel comp1View1
        longLabel comp1View1
        type bigWig
        view a

            track comp1Wig1
            bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.gc5Base.bw
            type bigWig
            subGroups view=A
            parent comp1View1

            track comp1Wig2
            bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.gc5Base.bw
            type bigWig
            subGroups view=A
            parent comp1View1

        track comp1View2
        parent comp1
        shortLabel comp1View2
        longLabel comp1View2
        type bigWig
        view b

            track comp1Wig3
            bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.gc5Base.bw
            type bigWig
            subGroups view=B
            parent comp1View2

            track comp1Wig4
            bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.gc5Base.bw
            type bigWig
            subGroups view=B
            parent comp1View2

    track comp2
    compositeTrack on
    shortLabel comp2
    longLabel comp2
    subGroup1 view Views A=a B=b
    type bigWig
    parent SuperTrackOfMultiWigsView

        track comp2View1
        view a
        shortLabel comp2View1
        longLabel comp2View1
        parent comp2
        type bigWig
    
            track comp2Wig1
            bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.gc5Base.bw
            type bigWig
            subGroups view=A
            parent comp2View1

            track comp2Wig2
            bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.gc5Base.bw
            type bigWig
            subGroups view=A
            parent comp2View1

        track comp2View2
        view b
        shortLabel comp2View1
        longLabel comp2View1
        parent comp2
        type bigWig

            track comp2Wig3
            bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.gc5Base.bw
            type bigWig
            subGroups view=B
            parent comp2View2

            track comp2Wig4
            bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.gc5Base.bw
            type bigWig
            subGroups view=B
            parent comp2View2

track BuildOverview
noInherit on
type bigBed 9
longLabel Ensembl Regulatory Build overviews
priority 1
dragAndDrop subTracks
compositeTrack on
html http://ftp.ensembl.org/pub/papers/regulation/mm10/overview/index
visibility squish
shortLabel Build Overview
#subGroup1 source Source dimY=source dimensions Regulatory_Build=EnsRegBuild Transcription_Factor_Binding_Site_Peaks_Summary=TFBS
#correct
subGroup1 source Source Regulatory_Build=EnsRegBuild Transcription_Factor_Binding_Site_Peaks_Summary=TFBS
#dimensions Regulatory_Build=EnsRegBuild Transcription_Factor_Binding_Site_Peaks_Summary=TFBS
sortOrder source=+

    track RegBuildOverview
    type bigBed 9
    longLabel Ensembl Regulatory label of regional function
    parent BuildOverview on
    bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.genscan.bb
    # wrong:
    #subGroups source=EnsRegBuild
    # correct
    #subGroups source=Regulatory_Build
    itemRgb on
    priority 1
    shortLabel Regulatory Build
    visibility squish

    track TFBSSummary
    type bigWig
    longLabel Summary of Transcription Factor Binding Site peaks from all cell types
    viewLimits 0:1
    color 209,157,0
    parent BuildOverview on
    bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.gc5Base.bw
    subGroups source=Transcription_Factor_Binding_Site_Peaks_Summary
    priority 3
    maxHeightPixels 128:64:16
    shortLabel TFBS Summary
    visibility full
    autoscale off

track MissingSubs
compositeTrack on
subGroup1 sub1 Sub1 tagA=valA tagB=valB
subGroup2 sub2 Sub2 tagC=valC tagD=valD
type bigBed 9
shortLabel TwoSubgroupDefs
longLabel Two Subgroup Definitions

    track track1
    shortLabel missingSub1
    longLabel Missing Subgroup1
    type bigBed 9
    bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.genscan.bb
    parent MissingSubs
    subGroups sub1=tagA sub2=tagD

    track track2
    shortLabel missingSub2
    longLabel Missing Subgroup2
    type bigBed 9
    bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.genscan.bb
    parent MissingSubs
    subGroups sub2=tagD


track multiWigExample
container multiWig
shortLabel multiWigExample
longLabel example Container MultiWig
type bigWig
autoScale on

    track multiWigSubtrack1
    bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.gc5Base.bw
    parent multiWigExample
    shortLabel wig1
    longLabel wig1

    track multiWigSubtrack2
    parent multiWigExample
    bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.gc5Base.bw
    shortLabel wig2
    longLabel wig2

    track multiWigSubtrack3
    parent multiWigExample
    bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.gc5Base.bw
    shortLabel wig3
    longLabel wig3

    track multiWigSubtrack4
    parent multiWigExample
    bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.gc5Base.bw
    shortLabel wig4
    longLabel wig4

    track multiWigSubtrack5
    parent multiWigExample
    bigDataUrl https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.gc5Base.bw
    shortLabel wig5
    longLabel wig5
