Mercurial > repos > iuc > jbrowse
diff test-data/gff3/test.xml @ 40:d5e8d72c432a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 7be399c9ee10ecd4b076cc1df775f585c3eb0eeb
| author | iuc |
|---|---|
| date | Wed, 01 Mar 2017 23:06:18 -0500 |
| parents | 6bfd32bd1000 |
| children | c1451868f8d4 |
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--- a/test-data/gff3/test.xml Thu Feb 09 12:36:02 2017 -0500 +++ b/test-data/gff3/test.xml Wed Mar 01 23:06:18 2017 -0500 @@ -3,268 +3,226 @@ <metadata> <gencode>11</gencode> <genomes> - <genome>test-data/merlin.fa</genome> + <genome>test-data/merlin.fa</genome> </genomes> <general> <defaultLocation></defaultLocation> - <trackPadding>20</trackPadding> - + <trackPadding>40</trackPadding> <shareLink>true</shareLink> <aboutDescription></aboutDescription> <show_tracklist>true</show_tracklist> <show_nav>true</show_nav> - <show_overview>true</show_overview> + <show_overview>false</show_overview> <show_menu>true</show_menu> <hideGenomeOptions>false</hideGenomeOptions> </general> </metadata> <tracks> - <track cat="Auto Coloured" format="gene_calls" visibility="default_off"> + <track cat="#date# / Auto Coloured" format="gene_calls" visibility="default_on"> <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"/> + <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>note,description</description> + <description>feature</description> <label>name,id</label> <height>100px</height> </style> + <gff> + </gff> <scaling> - <method>ignore</method> - <scheme> - <color>__auto__</color> - </scheme> + <method>ignore</method> + <scheme> + <color>__auto__</color> + </scheme> </scaling> - <menus> - </menus> - - <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> - <index>false</index> - </gff> </options> </track> - <track cat="Ignore Scale" format="gene_calls" visibility="default_off"> + <track cat="Ignore Scale" format="gene_calls"> <files> - <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/> + <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/> </files> <options> <style> <className>feature</className> - <description>note,description</description> + <description>feature</description> <label>name,id</label> <height>100px</height> </style> + <gff> + </gff> <scaling> - <method>ignore</method> - <scheme> - <color>#ff00ff</color> - </scheme> + <method>ignore</method> + <scheme> + <color>#ff00ff</color> + </scheme> </scaling> - <menus> - </menus> - - <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> - <index>false</index> - </gff> </options> </track> - <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> + <track cat="Scaled Colour" format="gene_calls"> <files> - <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/> + <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/> </files> <options> <style> <className>feature</className> - <description>note,description</description> + <description>feature</description> <label>name,id</label> <height>100px</height> </style> + <gff> + </gff> <scaling> - <method>score</method> - <algo>linear</algo> - <scales> - <type>automatic</type> - - </scales> - <scheme> - <type>opacity</type> - <color>__auto__</color> - </scheme> + <method>score</method> + <algo>linear</algo> + <scales> + <type>__auto__</type> + </scales> + <scheme> + <type>opacity</type> + <color>__auto__</color> + </scheme> </scaling> - <menus> - </menus> - - <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> - <index>false</index> - </gff> </options> </track> - <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> + <track cat="Scaled Colour" format="gene_calls"> <files> - <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds, Fixed Color"/> + <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds, Fixed Color"/> </files> <options> <style> <className>feature</className> - <description>note,description</description> + <description>feature</description> <label>name,id</label> <height>100px</height> </style> + <gff> + </gff> <scaling> - <method>score</method> - <algo>linear</algo> - <scales> - <type>automatic</type> - - </scales> - <scheme> - <type>opacity</type> - <color>#0000ff</color> - </scheme> + <method>score</method> + <algo>linear</algo> + <scales> + <type>__auto__</type> + </scales> + <scheme> + <type>opacity</type> + <color>#0000ff</color> + </scheme> </scaling> - <menus> - </menus> - - <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> - <index>false</index> - </gff> </options> </track> - <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> + <track cat="Scaled Colour" format="gene_calls"> <files> - <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/> + <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/> </files> <options> <style> <className>feature</className> - <description>note,description</description> + <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> + <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> - <menus> - </menus> - - <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> - <index>false</index> - </gff> </options> </track> - <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> + <track cat="Scaled Colour" format="gene_calls"> <files> - <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds, Fixed Color"/> + <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds, Fixed Color"/> </files> <options> <style> <className>feature</className> - <description>note,description</description> + <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> + <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> - <menus> - </menus> - - <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> - <index>false</index> - </gff> </options> </track> - <track cat="Realistic" format="gene_calls" visibility="default_off"> + + + <track cat="Realistic" format="gene_calls"> <files> - <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/> + <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/> </files> <options> <style> <className>feature</className> - <description>note,description</description> + <description>feature</description> <label>name,id</label> <height>100px</height> </style> + <gff> + </gff> <scaling> - <method>ignore</method> - <scheme> - <color>__auto__</color> - </scheme> + <method>ignore</method> + <scheme> + <color>__auto__</color> + </scheme> </scaling> - <menus> - </menus> - - <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> - <index>false</index> - </gff> </options> </track> - <track cat="Realistic" format="gene_calls" visibility="default_off"> + <track cat="Realistic" format="gene_calls"> <files> - <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/> + <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/> </files> <options> <style> <className>feature</className> - <description>note,description</description> + <description>feature</description> <label>name,id</label> <height>100px</height> </style> + <gff> + <match>cDNA_match</match> + </gff> <scaling> - <method>ignore</method> - <scheme> - <color>__auto__</color> - </scheme> + <method>ignore</method> + <scheme> + <type>opacity</type> + <color>__auto__</color> + </scheme> </scaling> - <menus> - </menus> - - <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> - <match>cDNA_match</match> - <index>false</index> - </gff> </options> </track> </tracks>