Mercurial > repos > iuc > jbrowse
diff test-data/gff3/test.xml @ 3:7342f467507b draft
Uploaded v0.4 of JBrowse
| author | iuc |
|---|---|
| date | Thu, 31 Dec 2015 13:58:43 -0500 |
| parents | |
| children | ae9382cfb6ac |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff3/test.xml Thu Dec 31 13:58:43 2015 -0500 @@ -0,0 +1,218 @@ +<?xml version="1.0"?> +<root> + <metadata> + <gencode>11</gencode> + <genomes> + <genome>test-data/merlin.fa</genome> + </genomes> + </metadata> + <tracks> + <track cat="Auto Coloured" format="gene_calls"> + <files> + <trackFile path="test-data/gff3/1.gff" ext="gff3" label="A"/> + <trackFile path="test-data/gff3/1.gff" ext="gff3" label="B"/> + <trackFile path="test-data/gff3/1.gff" ext="gff3" label="C"/> + <trackFile path="test-data/gff3/1.gff" ext="gff3" label="D"/> + </files> + + <options> + <style> + <className>feature</className> + <description>feature</description> + <label>name,id</label> + <height>100px</height> + </style> + <gff> + </gff> + <scaling> + <method>ignore</method> + <scheme> + <color>__auto__</color> + </scheme> + </scaling> + </options> + </track> + <track cat="Ignore Scale" format="gene_calls"> + <files> + <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/> + </files> + + <options> + <style> + <className>feature</className> + <description>feature</description> + <label>name,id</label> + <height>100px</height> + </style> + <gff> + </gff> + <scaling> + <method>ignore</method> + <scheme> + <color>#ff00ff</color> + </scheme> + </scaling> + </options> + </track> + <track cat="Scaled Colour" format="gene_calls"> + <files> + <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/> + </files> + + <options> + <style> + <className>feature</className> + <description>feature</description> + <label>name,id</label> + <height>100px</height> + </style> + <gff> + </gff> + <scaling> + <method>score</method> + <algo>linear</algo> + <scales> + <type>__auto__</type> + </scales> + <scheme> + <type>opacity</type> + <color>__auto__</color> + </scheme> + </scaling> + </options> + </track> + <track cat="Scaled Colour" format="gene_calls"> + <files> + <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds, Fixed Color"/> + </files> + + <options> + <style> + <className>feature</className> + <description>feature</description> + <label>name,id</label> + <height>100px</height> + </style> + <gff> + </gff> + <scaling> + <method>score</method> + <algo>linear</algo> + <scales> + <type>__auto__</type> + </scales> + <scheme> + <type>opacity</type> + <color>#0000ff</color> + </scheme> + </scaling> + </options> + </track> + <track cat="Scaled Colour" format="gene_calls"> + <files> + <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/> + </files> + + <options> + <style> + <className>feature</className> + <description>feature</description> + <label>name,id</label> + <height>100px</height> + </style> + <gff> + </gff> + <scaling> + <method>score</method> + <algo>linear</algo> + <scales> + <type>manual</type> + <min>0</min> + <max>1000</max> + </scales> + <scheme> + <type>opacity</type> + <color>__auto__</color> + </scheme> + </scaling> + </options> + </track> + <track cat="Scaled Colour" format="gene_calls"> + <files> + <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds, Fixed Color"/> + </files> + + <options> + <style> + <className>feature</className> + <description>feature</description> + <label>name,id</label> + <height>100px</height> + </style> + <gff> + </gff> + <scaling> + <method>score</method> + <algo>linear</algo> + <scales> + <type>manual</type> + <min>0</min> + <max>1000</max> + </scales> + <scheme> + <type>opacity</type> + <color>#ff0000</color> + </scheme> + </scaling> + </options> + </track> + + + <track cat="Realistic" format="gene_calls"> + <files> + <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/> + </files> + + <options> + <style> + <className>feature</className> + <description>feature</description> + <label>name,id</label> + <height>100px</height> + </style> + <gff> + </gff> + <scaling> + <method>ignore</method> + <scheme> + <color>__auto__</color> + </scheme> + </scaling> + </options> + </track> + <track cat="Realistic" format="gene_calls"> + <files> + <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/> + </files> + + <options> + <style> + <className>feature</className> + <description>feature</description> + <label>name,id</label> + <height>100px</height> + </style> + <gff> + <match>cDNA_match</match> + </gff> + <scaling> + <method>ignore</method> + <scheme> + <type>opacity</type> + <color>__auto__</color> + </scheme> + </scaling> + </options> + </track> + </tracks> +</root>