Mercurial > repos > iuc > jbrowse
changeset 29:112eb40ba6cf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit d51ab68aa8a806f7d5a3ebc00638a2486a98a214
| author | iuc |
|---|---|
| date | Fri, 05 Apr 2019 07:53:24 -0400 |
| parents | d0743cb18ed8 |
| children | ca2def38369c |
| files | jbrowse.xml test-data/gff3/test.xml |
| diffstat | 2 files changed, 38 insertions(+), 41 deletions(-) [+] |
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--- a/jbrowse.xml Fri Feb 22 03:20:59 2019 -0500 +++ b/jbrowse.xml Fri Apr 05 07:53:24 2019 -0400 @@ -130,7 +130,7 @@ display_name="${dataset.history.get_display_name()}"/> <metadata #for (key, value) in $dataset.get_metadata().items(): - #if "_types" not in $key: + #if "_types" not in $key and $value is not None and len(str($value)) < 20000: ${key}="${value}" #end if #end for
--- a/test-data/gff3/test.xml Fri Feb 22 03:20:59 2019 -0500 +++ b/test-data/gff3/test.xml Fri Apr 05 07:53:24 2019 -0400 @@ -3,7 +3,7 @@ <metadata> <gencode>11</gencode> <genomes> - <genome path="/tmp/tmpWtvfKr/files/000/dataset_5.dat"> + <genome path="/tmp/tmpTx5wXw/files/000/dataset_5.dat"> <metadata> <dataset id="7b55dbb89df8f4e5" hid="1" size="171.6 KB" @@ -42,7 +42,7 @@ <tracks> <track cat="Auto Coloured" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_6.dat" ext="gff3" label="A.gff"> + <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_6.dat" ext="gff3" label="gff3/A.gff"> <metadata> <dataset id="fa6d20d0fb68383f" hid="2" size="2.3 KB" @@ -57,7 +57,6 @@ data_lines="27" comment_lines="19" columns="9" - column_names="" delimiter="__tc__" attributes="6" /> @@ -67,7 +66,7 @@ /> </metadata> </trackFile> - <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_7.dat" ext="gff3" label="B.gff"> + <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_7.dat" ext="gff3" label="gff3/B.gff"> <metadata> <dataset id="683bc220e21425bb" hid="3" size="2.3 KB" @@ -82,7 +81,6 @@ data_lines="27" comment_lines="19" columns="9" - column_names="" delimiter="__tc__" attributes="6" /> @@ -92,7 +90,7 @@ /> </metadata> </trackFile> - <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_8.dat" ext="gff3" label="C.gff"> + <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_8.dat" ext="gff3" label="gff3/C.gff"> <metadata> <dataset id="a90a30fafe298e1e" hid="4" size="2.3 KB" @@ -107,7 +105,6 @@ data_lines="27" comment_lines="19" columns="9" - column_names="" delimiter="__tc__" attributes="6" /> @@ -117,7 +114,7 @@ /> </metadata> </trackFile> - <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_9.dat" ext="gff3" label="D.gff"> + <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_9.dat" ext="gff3" label="gff3/D.gff"> <metadata> <dataset id="b842d972534ccb3e" hid="5" size="2.3 KB" @@ -132,7 +129,6 @@ data_lines="27" comment_lines="19" columns="9" - column_names="" delimiter="__tc__" attributes="6" /> @@ -148,7 +144,7 @@ <style> <overridePlugins>False</overridePlugins> <overrideDraggable>False</overrideDraggable> - <className>feature</className> + <className>feature2</className> <description>note,description</description> <label>product,name,id</label> <height>10px</height> @@ -164,14 +160,15 @@ </menus> <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> + <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> + <topLevelFeatures>mRNA</topLevelFeatures> <index>false</index> </gff> </options> </track> <track cat="Ignore Scale" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_10.dat" ext="gff3" label="1.gff"> + <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_10.dat" ext="gff3" label="gff3/1.gff"> <metadata> <dataset id="5449172d6ff5669b" hid="6" size="2.3 KB" @@ -186,7 +183,6 @@ data_lines="27" comment_lines="19" columns="9" - column_names="" delimiter="__tc__" attributes="6" /> @@ -202,7 +198,7 @@ <style> <overridePlugins>False</overridePlugins> <overrideDraggable>False</overrideDraggable> - <className>feature</className> + <className>feature2</className> <description>note,description</description> <label>product,name,id</label> <height>10px</height> @@ -218,14 +214,15 @@ </menus> <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> + <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> + <topLevelFeatures>mRNA</topLevelFeatures> <index>false</index> </gff> </options> </track> <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_10.dat" ext="gff3" label="1.gff"> + <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_10.dat" ext="gff3" label="gff3/1.gff"> <metadata> <dataset id="5449172d6ff5669b" hid="6" size="2.3 KB" @@ -240,7 +237,6 @@ data_lines="27" comment_lines="19" columns="9" - column_names="" delimiter="__tc__" attributes="6" /> @@ -256,7 +252,7 @@ <style> <overridePlugins>False</overridePlugins> <overrideDraggable>False</overrideDraggable> - <className>feature</className> + <className>feature2</className> <description>note,description</description> <label>product,name,id</label> <height>10px</height> @@ -278,14 +274,15 @@ </menus> <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> + <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> + <topLevelFeatures>mRNA</topLevelFeatures> <index>false</index> </gff> </options> </track> <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_10.dat" ext="gff3" label="1.gff"> + <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_10.dat" ext="gff3" label="gff3/1.gff"> <metadata> <dataset id="5449172d6ff5669b" hid="6" size="2.3 KB" @@ -300,7 +297,6 @@ data_lines="27" comment_lines="19" columns="9" - column_names="" delimiter="__tc__" attributes="6" /> @@ -316,7 +312,7 @@ <style> <overridePlugins>False</overridePlugins> <overrideDraggable>False</overrideDraggable> - <className>feature</className> + <className>feature2</className> <description>note,description</description> <label>product,name,id</label> <height>10px</height> @@ -338,14 +334,15 @@ </menus> <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> + <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> + <topLevelFeatures>mRNA</topLevelFeatures> <index>false</index> </gff> </options> </track> <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_10.dat" ext="gff3" label="1.gff"> + <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_10.dat" ext="gff3" label="gff3/1.gff"> <metadata> <dataset id="5449172d6ff5669b" hid="6" size="2.3 KB" @@ -360,7 +357,6 @@ data_lines="27" comment_lines="19" columns="9" - column_names="" delimiter="__tc__" attributes="6" /> @@ -376,7 +372,7 @@ <style> <overridePlugins>False</overridePlugins> <overrideDraggable>False</overrideDraggable> - <className>feature</className> + <className>feature2</className> <description>note,description</description> <label>product,name,id</label> <height>10px</height> @@ -400,14 +396,15 @@ </menus> <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> + <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> + <topLevelFeatures>mRNA</topLevelFeatures> <index>false</index> </gff> </options> </track> <track cat="Scaled Colour" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_10.dat" ext="gff3" label="1.gff"> + <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_10.dat" ext="gff3" label="gff3/1.gff"> <metadata> <dataset id="5449172d6ff5669b" hid="6" size="2.3 KB" @@ -422,7 +419,6 @@ data_lines="27" comment_lines="19" columns="9" - column_names="" delimiter="__tc__" attributes="6" /> @@ -438,7 +434,7 @@ <style> <overridePlugins>False</overridePlugins> <overrideDraggable>False</overrideDraggable> - <className>feature</className> + <className>feature2</className> <description>note,description</description> <label>product,name,id</label> <height>10px</height> @@ -462,14 +458,15 @@ </menus> <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> + <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> + <topLevelFeatures>mRNA</topLevelFeatures> <index>false</index> </gff> </options> </track> <track cat="Realistic" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_11.dat" ext="gff3" label="interpro.gff"> + <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_11.dat" ext="gff3" label="gff3/interpro.gff"> <metadata> <dataset id="9ce08b2254e4d5ed" hid="7" size="103.3 KB" @@ -484,7 +481,6 @@ data_lines="556" comment_lines="2" columns="9" - column_names="" delimiter="__tc__" attributes="11" /> @@ -500,7 +496,7 @@ <style> <overridePlugins>False</overridePlugins> <overrideDraggable>False</overrideDraggable> - <className>feature</className> + <className>feature2</className> <description>note,description</description> <label>product,name,id</label> <height>10px</height> @@ -516,14 +512,15 @@ </menus> <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> + <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> + <topLevelFeatures>mRNA</topLevelFeatures> <index>false</index> </gff> </options> </track> <track cat="Realistic" format="gene_calls" visibility="default_off"> <files> - <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_12.dat" ext="gff3" label="2.gff"> + <trackFile path="/tmp/tmpTx5wXw/files/000/dataset_12.dat" ext="gff3" label="gff3/2.gff"> <metadata> <dataset id="80b8022ff3f677b7" hid="8" size="326 bytes" @@ -538,7 +535,6 @@ data_lines="3" comment_lines="3" columns="9" - column_names="" delimiter="__tc__" attributes="4" /> @@ -554,7 +550,7 @@ <style> <overridePlugins>False</overridePlugins> <overrideDraggable>False</overrideDraggable> - <className>feature</className> + <className>feature2</className> <description>note,description</description> <label>product,name,id</label> <height>10px</height> @@ -570,7 +566,8 @@ </menus> <gff> - <trackType>JBrowse/View/Track/CanvasFeatures</trackType> + <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> + <topLevelFeatures>mRNA</topLevelFeatures> <match>cDNA_match</match> <index>false</index> </gff> @@ -584,4 +581,4 @@ BlastView="True" theme="" /> -</root> +</root> \ No newline at end of file