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Visualization framework: add config files for built-in visualiztions

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Carl Eberhard
2013-08-07 11:48:25 -04:00
parent 744420c911
commit 0077144e37
4 changed files with 105 additions and 0 deletions
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config/plugins/visualizations/circster/config/circster.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="circster">
<data_sources>
<data_source>
<model_class>HistoryDatasetAssociation</model_class>
<test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
<to_param param_attr="id">dataset_id</to_param>
<to_param assign="hda">hda_ldda</to_param>
</data_source>
<data_source>
<model_class>LibraryDatasetDatasetAssociation</model_class>
<test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
<to_param param_attr="id">dataset_id</to_param>
<to_param assign="ldda">hda_ldda</to_param>
</data_source>
</data_sources>
<params>
<param type="visualization">id</param>
<param type="hda_or_ldda">dataset_id</param>
<param_modifier type="string" modifies="dataset_id">hda_ldda</param_modifier>
<param type="dbkey">dbkey</param>
</params>
<!-- template_root and template are currently ignored for the 'built-in' visualizations -->
<template_root>webapps/galaxy/visualization</template_root>
<template>circster.mako</template>
<render_location>_top</render_location>
</visualization>
config/plugins/visualizations/phyloviz/config/phyloviz.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="phyloviz">
<data_sources>
<data_source>
<model_class>HistoryDatasetAssociation</model_class>
<test type="isinstance" test_attr="datatype" result_type="datatype">data.Newick</test>
<test type="isinstance" test_attr="datatype" result_type="datatype">data.Nexus</test>
<to_param param_attr="id">dataset_id</to_param>
</data_source>
</data_sources>
<params>
<param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
<param type="integer" default="0">tree_index</param>
</params>
<!-- template_root and template are currently ignored for the 'built-in' visualizations -->
<template_root>webapps/galaxy/visualization</template_root>
<template>phyloviz.mako</template>
<render_location>_top</render_location>
</visualization>
config/plugins/visualizations/sweepster/config/sweepster.xml
+27
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="sweepster">
<data_sources>
<data_source>
<model_class>HistoryDatasetAssociation</model_class>
<test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
<to_param param_attr="id">dataset_id</to_param>
<to_param assign="hda">hda_ldda</to_param>
</data_source>
<data_source>
<model_class>LibraryDatasetDatasetAssociation</model_class>
<test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
<to_param param_attr="id">dataset_id</to_param>
<to_param assign="ldda">hda_ldda</to_param>
</data_source>
</data_sources>
<params>
<param type="visualization" var_name_in_template="viz">visualization</param>
<param type="hda_or_ldda" var_name_in_template="dataset">dataset_id</param>
<param_modifier type="string" modifies="dataset_id">hda_ldda</param_modifier>
</params>
<!-- template_root and template are currently ignored for the 'built-in' visualizations -->
<template_root>webapps/galaxy/visualization</template_root>
<template>sweepster.mako</template>
<render_location>_top</render_location>
</visualization>
config/plugins/visualizations/trackster/config/trackster.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
<visualization name="trackster">
<!--not tested yet -->
<data_sources>
<data_source>
<model_class>HistoryDatasetAssociation</model_class>
<test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
<to_param param_attr="id">dataset_id</to_param>
<to_param assign="hda">hda_ldda</to_param>
<to_param param_attr="dbkey">dbkey</to_param>
</data_source>
<data_source>
<model_class>LibraryDatasetDatasetAssociation</model_class>
<test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
<to_param param_attr="id">dataset_id</to_param>
<to_param assign="ldda">hda_ldda</to_param>
</data_source>
</data_sources>
<params>
<param type="visualization">id</param>
<param type="dataset">dataset_id</param>
<param type="genome_region">genome_region</param>
<param type="dbkey">dbkey</param>
</params>
<!-- template_root and template are currently ignored for the 'built-in' visualizations -->
<template_root>webapps/galaxy/visualization/tracks</template_root>
<template>browser.mako</template>
<render_location>_top</render_location>
</visualization>