1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/aa9aeb756031/ Changeset: aa9aeb756031 User: carlfeberhard Date: 2013-08-07 17:48:25 Summary: Visualization framework: add config files for built-in visualiztions Affected #: 4 files diff -r 425272160a7f3764823e18ea395539c54c8e41fd -r aa9aeb756031a63f4cd7dc4e1b2d84b12522ffef config/plugins/visualizations/circster/config/circster.xml --- /dev/null +++ b/config/plugins/visualizations/circster/config/circster.xml @@ -0,0 +1,28 @@ +<?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> diff -r 425272160a7f3764823e18ea395539c54c8e41fd -r aa9aeb756031a63f4cd7dc4e1b2d84b12522ffef config/plugins/visualizations/phyloviz/config/phyloviz.xml --- /dev/null +++ b/config/plugins/visualizations/phyloviz/config/phyloviz.xml @@ -0,0 +1,20 @@ +<?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> diff -r 425272160a7f3764823e18ea395539c54c8e41fd -r aa9aeb756031a63f4cd7dc4e1b2d84b12522ffef config/plugins/visualizations/sweepster/config/sweepster.xml --- /dev/null +++ b/config/plugins/visualizations/sweepster/config/sweepster.xml @@ -0,0 +1,27 @@ +<?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> diff -r 425272160a7f3764823e18ea395539c54c8e41fd -r aa9aeb756031a63f4cd7dc4e1b2d84b12522ffef config/plugins/visualizations/trackster/config/trackster.xml --- /dev/null +++ b/config/plugins/visualizations/trackster/config/trackster.xml @@ -0,0 +1,30 @@ +<?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> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from 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