Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fa3a2371e1b2873456a3034874036d9b8cadd01c https://github.com/galaxyproject/galaxy/commit/fa3a2371e1b2873456a3034874036... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-02-04 (Sun, 04 Feb 2018)
Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py
Log Message: ----------- WIP: add a SelectTagParameter
Commit: 4afbdbab31791101578be08acc3526e04c1835d6 https://github.com/galaxyproject/galaxy/commit/4afbdbab31791101578be08acc352... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-02-04 (Sun, 04 Feb 2018)
Changed paths: M test/unit/test_objectstore.py M test/unit/tools/test_wrappers.py
Log Message: ----------- Fix unit tests
Commit: 04b0cfcc1388de18aeb93a39fa44451009bbd67f https://github.com/galaxyproject/galaxy/commit/04b0cfcc1388de18aeb93a39fa444... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-02-07 (Wed, 07 Feb 2018)
Changed paths: M lib/galaxy/tools/wrappers.py
Log Message: ----------- Make `get_datasets_for_group` case insensitive to tag
Commit: 45b2b7f434fc1bd1e646c72c6024bacc482a8b8e https://github.com/galaxyproject/galaxy/commit/45b2b7f434fc1bd1e646c72c6024b... Author: John Chilton jmchilton@gmail.com Date: 2018-07-24 (Tue, 24 Jul 2018)
Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M CONTRIBUTING.md M Makefile M README.rst M client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-buttons.md A client/galaxy/docs/galaxy-forms.md A client/galaxy/docs/galaxy-masthead.md A client/galaxy/docs/galaxy-menus.md A client/galaxy/docs/galaxy-messages.md A client/galaxy/docs/galaxy-panels.md A client/galaxy/docs/galaxy-tables.md A client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/DataDialog.vue A client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/HistoryView.vue A client/galaxy/scripts/components/PluginList.vue A client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/RulesDisplay.vue A client/galaxy/scripts/components/Sharing.vue A client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/DataTypes.vue R client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.pages.js A client/galaxy/scripts/layout/communication-server-view.js A client/galaxy/scripts/layout/data.js R client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/legacy/grid/grid-view.js R client/galaxy/scripts/libs/bootstrap-tour.js R client/galaxy/scripts/libs/bootstrap.js A client/galaxy/scripts/mocha/test.js A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml A client/galaxy/scripts/mocha/tests/rules_tests.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js R client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/list/list-view.js A client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js A client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js A client/galaxy/scripts/mvc/visualization/chart/chart-client.js A client/galaxy/scripts/mvc/visualization/chart/components/model.js A client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js A client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js A client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js A client/galaxy/scripts/mvc/visualization/chart/utilities/series.js A client/galaxy/scripts/mvc/visualization/chart/views/description.js A client/galaxy/scripts/mvc/visualization/chart/views/editor.js A client/galaxy/scripts/mvc/visualization/chart/views/groups.js A client/galaxy/scripts/mvc/visualization/chart/views/menu.js A client/galaxy/scripts/mvc/visualization/chart/views/settings.js A client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/reports/run_stats.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/utils/async-save-text.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js R client/galaxy/style/less/autocomplete_tagging.less R client/galaxy/style/less/base.less R client/galaxy/style/less/bootstrap.less R client/galaxy/style/less/bootstrap/alerts.less R client/galaxy/style/less/bootstrap/badges.less R client/galaxy/style/less/bootstrap/bootstrap.less R client/galaxy/style/less/bootstrap/breadcrumbs.less R client/galaxy/style/less/bootstrap/button-groups.less R client/galaxy/style/less/bootstrap/buttons.less R client/galaxy/style/less/bootstrap/carousel.less R client/galaxy/style/less/bootstrap/close.less R client/galaxy/style/less/bootstrap/code.less R client/galaxy/style/less/bootstrap/component-animations.less R client/galaxy/style/less/bootstrap/dropdowns.less R client/galaxy/style/less/bootstrap/forms.less R client/galaxy/style/less/bootstrap/glyphicons.less R client/galaxy/style/less/bootstrap/grid.less R client/galaxy/style/less/bootstrap/input-groups.less R client/galaxy/style/less/bootstrap/jumbotron.less R client/galaxy/style/less/bootstrap/labels.less R client/galaxy/style/less/bootstrap/list-group.less R client/galaxy/style/less/bootstrap/media.less R client/galaxy/style/less/bootstrap/mixins.less R client/galaxy/style/less/bootstrap/modals.less R client/galaxy/style/less/bootstrap/navbar.less R client/galaxy/style/less/bootstrap/navs.less R client/galaxy/style/less/bootstrap/normalize.less R client/galaxy/style/less/bootstrap/pager.less R client/galaxy/style/less/bootstrap/pagination.less R client/galaxy/style/less/bootstrap/panels.less R client/galaxy/style/less/bootstrap/popovers.less R client/galaxy/style/less/bootstrap/print.less R client/galaxy/style/less/bootstrap/progress-bars.less R client/galaxy/style/less/bootstrap/responsive-utilities.less R client/galaxy/style/less/bootstrap/scaffolding.less R client/galaxy/style/less/bootstrap/tables.less R client/galaxy/style/less/bootstrap/theme.less R client/galaxy/style/less/bootstrap/thumbnails.less R client/galaxy/style/less/bootstrap/tooltip.less R client/galaxy/style/less/bootstrap/type.less R client/galaxy/style/less/bootstrap/utilities.less R client/galaxy/style/less/bootstrap/variables.less R client/galaxy/style/less/bootstrap/wells.less R client/galaxy/style/less/circster.less R client/galaxy/style/less/collection.less R client/galaxy/style/less/dataset.less R client/galaxy/style/less/embed_item.less R client/galaxy/style/less/flex.less R client/galaxy/style/less/fontawesome/bordered-pulled.less R client/galaxy/style/less/fontawesome/core.less R client/galaxy/style/less/fontawesome/fixed-width.less R client/galaxy/style/less/fontawesome/font-awesome.less R client/galaxy/style/less/fontawesome/icons.less R client/galaxy/style/less/fontawesome/larger.less R client/galaxy/style/less/fontawesome/list.less R client/galaxy/style/less/fontawesome/mixins.less R client/galaxy/style/less/fontawesome/path.less R client/galaxy/style/less/fontawesome/rotated-flipped.less R client/galaxy/style/less/fontawesome/spinning.less R client/galaxy/style/less/fontawesome/stacked.less R client/galaxy/style/less/fontawesome/variables.less R client/galaxy/style/less/frame.less R client/galaxy/style/less/galaxy_bootstrap.less R client/galaxy/style/less/galaxy_bootstrap/overrides.less R client/galaxy/style/less/galaxy_bootstrap/variables.less R client/galaxy/style/less/galaxy_variables.less R client/galaxy/style/less/history.less R client/galaxy/style/less/iconic_stroke.less R client/galaxy/style/less/job.less R client/galaxy/style/less/jstree.less R client/galaxy/style/less/library.less R client/galaxy/style/less/list-item.less R client/galaxy/style/less/reports.less R client/galaxy/style/less/select2.less R client/galaxy/style/less/theme/blue.less R client/galaxy/style/less/theme/plain.less R client/galaxy/style/less/toastr.less R client/galaxy/style/less/tour.less R client/galaxy/style/less/trackster.less R client/galaxy/style/less/ui.less R client/galaxy/style/less/ui/dataset-choice.less R client/galaxy/style/less/ui/error-modal.less R client/galaxy/style/less/ui/icon-btn.less R client/galaxy/style/less/ui/pagination.less R client/galaxy/style/less/ui/paired-collection-creator.less R client/galaxy/style/less/ui/peek-column-selector.less R client/galaxy/style/less/ui/search-input.less R client/galaxy/style/less/upload.less A client/galaxy/style/scss/autocomplete_tagging.scss A client/galaxy/style/scss/base.scss A client/galaxy/style/scss/charts.scss A client/galaxy/style/scss/circster.scss A client/galaxy/style/scss/collection.scss A client/galaxy/style/scss/dataset.scss A client/galaxy/style/scss/embed_item.scss A client/galaxy/style/scss/flex.scss A client/galaxy/style/scss/frame.scss A client/galaxy/style/scss/galaxy_bootstrap/overrides.scss A client/galaxy/style/scss/galaxy_bootstrap/variables.scss A client/galaxy/style/scss/galaxy_variables.scss A client/galaxy/style/scss/history.scss A client/galaxy/style/scss/iconic_stroke.scss A client/galaxy/style/scss/job.scss A client/galaxy/style/scss/jstree.scss A client/galaxy/style/scss/library.scss A client/galaxy/style/scss/list-item.scss A client/galaxy/style/scss/reports.scss A client/galaxy/style/scss/select2.scss A client/galaxy/style/scss/theme/blue.scss A client/galaxy/style/scss/theme/plain.scss A client/galaxy/style/scss/toastr.scss A client/galaxy/style/scss/tour.scss A client/galaxy/style/scss/trackster.scss A client/galaxy/style/scss/ui.scss A client/galaxy/style/scss/ui/dataset-choice.scss A client/galaxy/style/scss/ui/error-modal.scss A client/galaxy/style/scss/ui/icon-btn.scss A client/galaxy/style/scss/ui/pagination.scss A client/galaxy/style/scss/ui/paired-collection-creator.scss A client/galaxy/style/scss/ui/peek-column-selector.scss A client/galaxy/style/scss/ui/search-input.scss A client/galaxy/style/scss/upload.scss R client/grunt-tasks/style.js M client/gulpfile.js M client/karma.config.js M client/package.json A client/styleguide.config.js M client/webpack.config.js M client/yarn.lock M config/containers_conf.yml.sample M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/job_conf.xml.sample_basic M config/job_metrics_conf.xml.sample M config/local_conda_mapping.yml.sample A config/oidc_backends_config.xml.sample A config/oidc_config.xml.sample M config/openid_conf.xml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/tours/core.scratchbook.yaml R config/plugins/visualizations/charts/config/charts.xml R config/plugins/visualizations/charts/package.json R config/plugins/visualizations/charts/static/client/app.css R config/plugins/visualizations/charts/static/client/app.js R config/plugins/visualizations/charts/static/client/components/model.js R config/plugins/visualizations/charts/static/client/components/screenshot.js R config/plugins/visualizations/charts/static/client/views/description.js R config/plugins/visualizations/charts/static/client/views/editor.js R config/plugins/visualizations/charts/static/client/views/groups.js R config/plugins/visualizations/charts/static/client/views/settings.js R config/plugins/visualizations/charts/static/client/views/viewer.js R config/plugins/visualizations/charts/static/client/views/viewport.js R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map R config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js R config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map R config/plugins/visualizations/charts/static/repository/build/biojs_msa.js R config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map R config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js R config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map R config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js R config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js R config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js R config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_line.js R config/plugins/visualizations/charts/static/repository/build/jqplot_line.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js R config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js.map R config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js R config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_line.js R config/plugins/visualizations/charts/static/repository/build/nvd3_line.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js R config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js R config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js R config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js.map R config/plugins/visualizations/charts/static/repository/build/others_example.js R config/plugins/visualizations/charts/static/repository/build/others_example.js.map R config/plugins/visualizations/charts/static/repository/build/others_heatmap.js R config/plugins/visualizations/charts/static/repository/build/others_heatmap.js.map R config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js R config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js.map R config/plugins/visualizations/charts/static/repository/build/pv_viewer.js R config/plugins/visualizations/charts/static/repository/build/pv_viewer.js.map R config/plugins/visualizations/charts/static/repository/build/registry.js R config/plugins/visualizations/charts/static/repository/build/registry.js.map R config/plugins/visualizations/charts/static/repository/build/registry.tmp.js R config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css R config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/biojs.msa.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/drawrna.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/layout.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/base.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/connection.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/getnaview.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/loop.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/naview.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/radloop.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/region.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/radiate/getradiate.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js R config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js R config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js R config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css R config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js R config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js R config/plugins/visualizations/charts/static/repository/registry.json R config/plugins/visualizations/charts/static/repository/utilities/jobs.js R config/plugins/visualizations/charts/static/repository/utilities/sifjson.js R config/plugins/visualizations/charts/static/repository/utilities/utils.js R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js R config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js R config/plugins/visualizations/charts/templates/charts.mako R config/plugins/visualizations/charts/webpack.config.js A config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/logo.png M config/plugins/visualizations/csg/templates/csg.mako A config/plugins/visualizations/cytoscape/config/cytoscape.xml A config/plugins/visualizations/cytoscape/package.json A config/plugins/visualizations/cytoscape/src/script.js A config/plugins/visualizations/cytoscape/static/logo.png A config/plugins/visualizations/cytoscape/static/script.js A config/plugins/visualizations/drawrna/config/drawrna.xml A config/plugins/visualizations/drawrna/package.json A config/plugins/visualizations/drawrna/src/drawrnajs/drawrna.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/layout.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/base.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/connection.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/getnaview.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/loop.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/naview.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/radloop.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/region.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/radiate/getradiate.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/link.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/linkcol.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/ncanno.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/residue.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/residuecol.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/structure.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/.Rhistory A config/plugins/visualizations/drawrna/src/drawrnajs/utils/lasso.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/parsedbr.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/spectrum.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/style.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/annoview.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/optspanel.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/seqpanel.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/vispanel.js A config/plugins/visualizations/drawrna/src/script.js A config/plugins/visualizations/drawrna/static/logo.png A config/plugins/visualizations/drawrna/static/script.js A config/plugins/visualizations/example/config/example.xml A config/plugins/visualizations/example/package.json A config/plugins/visualizations/example/src/script.js A config/plugins/visualizations/example/static/logo.png A config/plugins/visualizations/example/static/script.js M config/plugins/visualizations/graphviz/config/graphviz.xml R config/plugins/visualizations/graphviz/static/js/jquery.qtip.js R config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js R config/plugins/visualizations/graphviz/static/js/tip_followscroll.js M config/plugins/visualizations/graphviz/templates/graphviz.mako A config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml A config/plugins/visualizations/heatmap/heatmap_cluster/static/logo.png A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml A config/plugins/visualizations/heatmap/heatmap_default/package.json A config/plugins/visualizations/heatmap/heatmap_default/src/colorsets.js A config/plugins/visualizations/heatmap/heatmap_default/src/script.js A config/plugins/visualizations/heatmap/heatmap_default/static/logo.png A config/plugins/visualizations/heatmap/heatmap_default/static/script.js A config/plugins/visualizations/hivtrace/config/hivtrace.xml A config/plugins/visualizations/hivtrace/static/448c34a56d699c29117adc64c43affeb.woff2 A config/plugins/visualizations/hivtrace/static/674f50d287a8c48dc19ba404d20fe713.eot A config/plugins/visualizations/hivtrace/static/89889688147bd7575d6327160d64e760.svg A config/plugins/visualizations/hivtrace/static/912ec66d7572ff821749319396470bde.svg A config/plugins/visualizations/hivtrace/static/af7ae505a9eed503f8b8e6982036873e.woff2 A config/plugins/visualizations/hivtrace/static/b06871f281fee6b241d60582ae9369b9.ttf A config/plugins/visualizations/hivtrace/static/e18bbf611f2a2e43afc071aa2f4e1512.ttf A config/plugins/visualizations/hivtrace/static/f4769f9bdb7466be65088239c12046d1.eot A config/plugins/visualizations/hivtrace/static/fa2772327f55d8198301fdb8bcfc8158.woff A config/plugins/visualizations/hivtrace/static/fee66e712a8a08eef5805a46892932ad.woff A config/plugins/visualizations/hivtrace/static/hivtrace.css A config/plugins/visualizations/hivtrace/static/hivtrace.css.map A config/plugins/visualizations/hivtrace/static/hivtrace.js A config/plugins/visualizations/hivtrace/static/hivtrace.js.map A config/plugins/visualizations/hivtrace/static/logo.png A config/plugins/visualizations/hivtrace/static/vendor.js A config/plugins/visualizations/hivtrace/static/vendor.js.map A config/plugins/visualizations/hivtrace/templates/index.mako A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_shared.xml A config/plugins/visualizations/jqplot/jqplot_bar/package.json A config/plugins/visualizations/jqplot/jqplot_bar/src/script.js A config/plugins/visualizations/jqplot/jqplot_bar/static/logo.png A config/plugins/visualizations/jqplot/jqplot_bar/static/script.css A config/plugins/visualizations/jqplot/jqplot_bar/static/script.js A config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml A config/plugins/visualizations/jqplot/jqplot_box/static/logo.png A config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml A config/plugins/visualizations/jqplot/jqplot_histogram/static/logo.png A config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml A config/plugins/visualizations/jqplot/jqplot_line/static/logo.png A config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml A config/plugins/visualizations/jqplot/jqplot_scatter/static/logo.png A config/plugins/visualizations/msa/config/msa.xml A config/plugins/visualizations/msa/package.json A config/plugins/visualizations/msa/src/msa.js A config/plugins/visualizations/msa/static/logo.png A config/plugins/visualizations/msa/static/script.js A config/plugins/visualizations/ngl/config/ngl.xml A config/plugins/visualizations/ngl/package.json A config/plugins/visualizations/ngl/src/ngl.js A config/plugins/visualizations/ngl/src/viewer.js A config/plugins/visualizations/ngl/static/logo.png A config/plugins/visualizations/ngl/static/ngl.js A config/plugins/visualizations/nvd3/nvd3_bar/.babelrc A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml A config/plugins/visualizations/nvd3/nvd3_bar/package.json A config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js A config/plugins/visualizations/nvd3/nvd3_bar/static/logo.png A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.css A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js A config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml A config/plugins/visualizations/nvd3/nvd3_bar_stacked/static/logo.png A config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml A config/plugins/visualizations/nvd3/nvd3_histogram/static/logo.png A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/static/logo.png A config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml A config/plugins/visualizations/nvd3/nvd3_horizontal/static/logo.png A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/static/logo.png A config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml A config/plugins/visualizations/nvd3/nvd3_line/static/logo.png A config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml A config/plugins/visualizations/nvd3/nvd3_line_focus/static/logo.png A config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml A config/plugins/visualizations/nvd3/nvd3_pie/static/logo.png A config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml A config/plugins/visualizations/nvd3/nvd3_scatter/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/static/logo.png A config/plugins/visualizations/phylocanvas/config/phylocanvas.xml A config/plugins/visualizations/phylocanvas/package.json A config/plugins/visualizations/phylocanvas/src/script.js A config/plugins/visualizations/phylocanvas/static/logo.png A config/plugins/visualizations/phylocanvas/static/script.js M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png A config/plugins/visualizations/pv/config/pv.xml A config/plugins/visualizations/pv/package.json A config/plugins/visualizations/pv/src/pv.js A config/plugins/visualizations/pv/static/logo.png A config/plugins/visualizations/pv/static/pv.js A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js A config/plugins/visualizations/scatterplot/src/numeric-column-stats.js M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/src/worker-stats.js A config/plugins/visualizations/scatterplot/static/8850628034555be072a0e4f882d4d8e5.js A config/plugins/visualizations/scatterplot/static/logo.png R config/plugins/visualizations/scatterplot/static/numeric-column-stats.js R config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js A config/plugins/visualizations/scatterplot/static/scatterplot.js R config/plugins/visualizations/scatterplot/static/worker-stats.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R config/plugins/visualizations/scatterplot/webpack.config.js M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png M config/plugins/visualizations/unipept/config/unipept.xml M config/plugins/visualizations/unipept/templates/unipept.mako A config/plugins/visualizations/venn/config/venn.xml A config/plugins/visualizations/venn/package.json A config/plugins/visualizations/venn/src/script.js A config/plugins/visualizations/venn/src/venn.js A config/plugins/visualizations/venn/static/logo.png A config/plugins/visualizations/venn/static/script.css A config/plugins/visualizations/venn/static/script.js M config/plugins/webhooks/demo/search/script.js M config/plugins/webhooks/demo/tour_generator/__init__.py M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_data_table_conf.xml.sample M config/tool_destinations.yml.sample M config/tool_shed.yml.sample M config/user_preferences_extra_conf.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M create_db.sh M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml A display_applications/intermine/intermine_simple.xml M doc/parse_gx_xsd.py M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/nginx.md M doc/source/admin/reports_options.rst M doc/source/admin/scaling.md M doc/source/admin/special_topics/bug_reports.rst A doc/source/admin/special_topics/gdpr_compliance.rst M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/performance_tracking.rst M doc/source/conf.py A doc/source/conf.versioning.py M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/project/organization.rst A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst M extract_dataset_parts.sh M lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py A lib/galaxy/authnz/__init__.py A lib/galaxy/authnz/managers.py A lib/galaxy/authnz/psa_authnz.py M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py R lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml A lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_fai.xml M lib/galaxy/datatypes/converters/fasta_to_len.py R lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml R lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml R lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py R lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.py A lib/galaxy/datatypes/converters/gz_to_uncompressed.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py R lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.afg A lib/galaxy/datatypes/test/1.arff A lib/galaxy/datatypes/test/1.fastqsanger.bz2 A lib/galaxy/datatypes/test/1.fastqsanger.gz A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz A lib/galaxy/datatypes/test/1.hdt A lib/galaxy/datatypes/test/1.obo A lib/galaxy/datatypes/test/1.owl A lib/galaxy/datatypes/test/1.phyloxml A lib/galaxy/datatypes/test/1.stockholm A lib/galaxy/datatypes/test/1.tiff A lib/galaxy/datatypes/test/1.ttl A lib/galaxy/datatypes/test/1.xmfa A lib/galaxy/datatypes/test/2.tabular A lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.txt A lib/galaxy/datatypes/test/Acanium.hmm A lib/galaxy/datatypes/test/diamond.daa A lib/galaxy/datatypes/test/empty.txt M lib/galaxy/datatypes/test/example.iqtree A lib/galaxy/datatypes/test/test.blib M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py A lib/galaxy/datatypes/upload_util.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conda-file.sh M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/dependencies/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile R lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/dynamic_tool_destination.py R lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py A lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py A lib/galaxy/jobs/metrics/instrumenters/hostname.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/job/torque.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py R lib/galaxy/jobs/runners/util/drmaa/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py R lib/galaxy/jobs/runners/util/retry.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py A lib/galaxy/managers/cloud.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py A lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py A lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/apply_rules.xml M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py A lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/data/__init__.py A lib/galaxy/tools/data_fetch.py A lib/galaxy/tools/data_fetch.xml M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/lmod.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py A lib/galaxy/tools/filter_empty_collection.xml M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/linters/command.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/cwl.py A lib/galaxy/tools/parser/error_level.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/relabel_from_file.xml M lib/galaxy/tools/repositories.py M lib/galaxy/tools/special_tools.py A lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/interactor.py A lib/galaxy/tools/verify/script.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py A lib/galaxy/util/create_history_template.py M lib/galaxy/util/facts.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py M lib/galaxy/util/monitors.py M lib/galaxy/util/none_like.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/permutations.py A lib/galaxy/util/rules_dsl.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/script.py M lib/galaxy/util/validation.py A lib/galaxy/util/watcher.py M lib/galaxy/util/xml_macros.py M lib/galaxy/version.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py A lib/galaxy/web/framework/helpers/tags.py M lib/galaxy/web/framework/middleware/batch.py R lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/sentry.py A lib/galaxy/web/framework/middleware/sqldebug.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/config_manage.py A lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/annotations.py A lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py A lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py A lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/config_watchers.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py A lib/galaxy/webapps/galaxy/controllers/authnz.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/web_util.py M lib/tool_shed/util/workflow_util.py M manage_db.sh R openid/aol.xml M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/api/common.py A scripts/api/fetch_to_library.py A scripts/api/fetch_to_library_example.yml A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/check_python.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/common_startup_functions.sh R scripts/common_startup_variables.sh M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py A scripts/docker_swarm_manager.py M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/maintenance.sh M scripts/manage_db.py R scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/migrate_tools/migrate_tools.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh A scripts/plugin_staging.py M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py A static/images/fonts/FontAwesome.otf M static/images/fonts/fontawesome-webfont.eot A static/images/fonts/fontawesome-webfont.svg M static/images/fonts/fontawesome-webfont.ttf M static/images/fonts/fontawesome-webfont.woff A static/images/fonts/fontawesome-webfont.woff2 R static/scripts/admin.toolshed.js R static/scripts/bundled/admin.bundled.js R static/scripts/bundled/analysis.bundled.js R static/scripts/bundled/extended.bundled.js R static/scripts/bundled/libs.bundled.js R static/scripts/bundled/login.bundled.js R static/scripts/galaxy.interactive_environments.js R static/scripts/galaxy.js R static/scripts/galaxy.library.js R static/scripts/galaxy.pages.js R static/scripts/i18n.js R static/scripts/layout/generic-nav-view.js R static/scripts/layout/masthead.js R static/scripts/layout/menu.js R static/scripts/layout/modal.js R static/scripts/layout/page.js R static/scripts/layout/panel.js R static/scripts/layout/router.js R static/scripts/layout/scratchbook.js R static/scripts/legacy/grid/grid-model.js R static/scripts/legacy/grid/grid-template.js R static/scripts/legacy/grid/grid-view.js R static/scripts/libs/backbone.js R static/scripts/libs/bbi/bigwig.js R static/scripts/libs/bbi/jquery-ajax-native.js R static/scripts/libs/bbi/jszlib.js R static/scripts/libs/bbi/spans.js R static/scripts/libs/bibtexParse.js R static/scripts/libs/bootstrap-tour.js R static/scripts/libs/bootstrap.js R static/scripts/libs/d3.js R static/scripts/libs/farbtastic.js R static/scripts/libs/jquery.sparklines.js R static/scripts/libs/jquery/jquery-ui.js R static/scripts/libs/jquery/jquery.autocomplete.js R static/scripts/libs/jquery/jquery.complexify.js R static/scripts/libs/jquery/jquery.cookie.js R static/scripts/libs/jquery/jquery.dynatree.js R static/scripts/libs/jquery/jquery.event.drag.js R static/scripts/libs/jquery/jquery.event.drop.js R static/scripts/libs/jquery/jquery.event.hover.js R static/scripts/libs/jquery/jquery.form.js R static/scripts/libs/jquery/jquery.js R static/scripts/libs/jquery/jquery.migrate.js R static/scripts/libs/jquery/jquery.mousewheel.js R static/scripts/libs/jquery/jquery.rating.js R static/scripts/libs/jquery/jquery.wymeditor.js R static/scripts/libs/jquery/jstorage.js R static/scripts/libs/jquery/jstree.js R static/scripts/libs/jquery/select2.js R static/scripts/libs/raven.js R static/scripts/libs/require.js R static/scripts/libs/toastr.js R static/scripts/libs/underscore.js R static/scripts/mvc/annotation.js R static/scripts/mvc/base-mvc.js R static/scripts/mvc/base/controlled-fetch-collection.js R static/scripts/mvc/collection/base-creator.js R static/scripts/mvc/collection/collection-li-edit.js R static/scripts/mvc/collection/collection-li.js R static/scripts/mvc/collection/collection-model.js R static/scripts/mvc/collection/collection-view-edit.js R static/scripts/mvc/collection/collection-view.js R static/scripts/mvc/collection/list-collection-creator.js R static/scripts/mvc/collection/list-of-pairs-collection-creator.js R static/scripts/mvc/collection/pair-collection-creator.js R static/scripts/mvc/dataset/data.js R static/scripts/mvc/dataset/dataset-choice.js R static/scripts/mvc/dataset/dataset-edit-attributes.js R static/scripts/mvc/dataset/dataset-error.js R static/scripts/mvc/dataset/dataset-li-edit.js R static/scripts/mvc/dataset/dataset-li.js R static/scripts/mvc/dataset/dataset-list.js R static/scripts/mvc/dataset/dataset-model.js R static/scripts/mvc/dataset/states.js R static/scripts/mvc/form/form-data.js R static/scripts/mvc/form/form-input.js R static/scripts/mvc/form/form-parameters.js R static/scripts/mvc/form/form-repeat.js R static/scripts/mvc/form/form-section.js R static/scripts/mvc/form/form-view.js R static/scripts/mvc/form/form-wrapper.js R static/scripts/mvc/grid/grid-model.js R static/scripts/mvc/grid/grid-shared.js R static/scripts/mvc/grid/grid-template.js R static/scripts/mvc/grid/grid-view.js R static/scripts/mvc/history/copy-dialog.js R static/scripts/mvc/history/hda-li-edit.js R static/scripts/mvc/history/hda-li.js R static/scripts/mvc/history/hda-model.js R static/scripts/mvc/history/hdca-li-edit.js R static/scripts/mvc/history/hdca-li.js R static/scripts/mvc/history/hdca-model.js R static/scripts/mvc/history/history-content-model.js R static/scripts/mvc/history/history-contents.js R static/scripts/mvc/history/history-item-li.js R static/scripts/mvc/history/history-list.js R static/scripts/mvc/history/history-model.js R static/scripts/mvc/history/history-preferences.js R static/scripts/mvc/history/history-structure-view.js R static/scripts/mvc/history/history-view-annotated.js R static/scripts/mvc/history/history-view-edit-current.js R static/scripts/mvc/history/history-view-edit.js R static/scripts/mvc/history/history-view.js R static/scripts/mvc/history/job-dag.js R static/scripts/mvc/history/job-states-model.js R static/scripts/mvc/history/multi-panel.js R static/scripts/mvc/history/options-menu.js R static/scripts/mvc/job/job-li.js R static/scripts/mvc/job/job-model.js R static/scripts/mvc/job/job-params.js R static/scripts/mvc/lazy/lazy-limited.js R static/scripts/mvc/library/library-dataset-view.js R static/scripts/mvc/library/library-folder-view.js R static/scripts/mvc/library/library-folderlist-view.js R static/scripts/mvc/library/library-folderrow-view.js R static/scripts/mvc/library/library-foldertoolbar-view.js R static/scripts/mvc/library/library-library-view.js R static/scripts/mvc/library/library-librarylist-view.js R static/scripts/mvc/library/library-libraryrow-view.js R static/scripts/mvc/library/library-librarytoolbar-view.js R static/scripts/mvc/library/library-model.js R static/scripts/mvc/library/library-util.js R static/scripts/mvc/list/list-item.js R static/scripts/mvc/list/list-view.js R static/scripts/mvc/tag.js R static/scripts/mvc/tool/tool-form-base.js R static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form.js R static/scripts/mvc/tool/tool-genomespace.js R static/scripts/mvc/tool/tools.js R static/scripts/mvc/toolshed/categories-view.js R static/scripts/mvc/toolshed/repo-queue-view.js R static/scripts/mvc/toolshed/repo-status-view.js R static/scripts/mvc/toolshed/repositories-view.js R static/scripts/mvc/toolshed/repository-queue-view.js R static/scripts/mvc/toolshed/repository-view.js R static/scripts/mvc/toolshed/shed-list-view.js R static/scripts/mvc/toolshed/toolshed-model.js R static/scripts/mvc/toolshed/util.js R static/scripts/mvc/toolshed/workflows-view.js R static/scripts/mvc/tours.js R static/scripts/mvc/ui/error-modal.js R static/scripts/mvc/ui/icon-button.js R static/scripts/mvc/ui/popup-menu.js R static/scripts/mvc/ui/ui-buttons.js R static/scripts/mvc/ui/ui-color-picker.js R static/scripts/mvc/ui/ui-drilldown.js R static/scripts/mvc/ui/ui-frames.js R static/scripts/mvc/ui/ui-list.js R static/scripts/mvc/ui/ui-misc.js R static/scripts/mvc/ui/ui-modal.js R static/scripts/mvc/ui/ui-options.js R static/scripts/mvc/ui/ui-popover.js R static/scripts/mvc/ui/ui-portlet.js R static/scripts/mvc/ui/ui-select-content.js R static/scripts/mvc/ui/ui-select-default.js R static/scripts/mvc/ui/ui-select-ftp.js R static/scripts/mvc/ui/ui-select-genomespace.js R static/scripts/mvc/ui/ui-select-library.js R static/scripts/mvc/ui/ui-select.js R static/scripts/mvc/ui/ui-slider.js R static/scripts/mvc/ui/ui-table.js R static/scripts/mvc/ui/ui-tabs.js R static/scripts/mvc/ui/ui-thumbnails.js R static/scripts/mvc/upload/collection/collection-row.js R static/scripts/mvc/upload/collection/collection-view.js R static/scripts/mvc/upload/composite/composite-row.js R static/scripts/mvc/upload/composite/composite-view.js R static/scripts/mvc/upload/default/default-row.js R static/scripts/mvc/upload/default/default-view.js R static/scripts/mvc/upload/upload-button.js R static/scripts/mvc/upload/upload-extension.js R static/scripts/mvc/upload/upload-ftp.js R static/scripts/mvc/upload/upload-model.js R static/scripts/mvc/upload/upload-settings.js R static/scripts/mvc/upload/upload-view.js R static/scripts/mvc/user/user-custom-builds.js R static/scripts/mvc/user/user-model.js R static/scripts/mvc/user/user-preferences.js R static/scripts/mvc/user/user-quotameter.js R static/scripts/mvc/visualization/visualization-model.js R static/scripts/mvc/webhooks.js R static/scripts/mvc/workflow/workflow-canvas.js R static/scripts/mvc/workflow/workflow-connector.js R static/scripts/mvc/workflow/workflow-forms.js R static/scripts/mvc/workflow/workflow-icons.js R static/scripts/mvc/workflow/workflow-manager.js R static/scripts/mvc/workflow/workflow-model.js R static/scripts/mvc/workflow/workflow-node.js R static/scripts/mvc/workflow/workflow-terminals.js R static/scripts/mvc/workflow/workflow-view-data.js R static/scripts/mvc/workflow/workflow-view-node.js R static/scripts/mvc/workflow/workflow-view-terminals.js R static/scripts/mvc/workflow/workflow-view.js R static/scripts/mvc/workflow/workflow.js R static/scripts/nls/de/locale.js R static/scripts/nls/es/locale.js R static/scripts/nls/fr/locale.js R static/scripts/nls/ja/locale.js R static/scripts/nls/locale.js R static/scripts/nls/zh/locale.js R static/scripts/onload.js R static/scripts/packed R static/scripts/polyfills.js R static/scripts/reports/run_stats.js R static/scripts/toolshed/groups/group-detail-view.js R static/scripts/toolshed/groups/group-list-view.js R static/scripts/toolshed/groups/group-listrow-view.js R static/scripts/toolshed/groups/group-model.js R static/scripts/toolshed/toolshed.groups.js R static/scripts/ui/autocom_tagging.js R static/scripts/ui/editable-text.js R static/scripts/ui/fa-icon-button.js R static/scripts/ui/filter-control.js R static/scripts/ui/hoverhighlight.js R static/scripts/ui/loading-indicator.js R static/scripts/ui/mode-button.js R static/scripts/ui/pagination.js R static/scripts/ui/peek-column-selector.js R static/scripts/ui/popupmenu.js R static/scripts/ui/scroll-panel.js R static/scripts/ui/search-input.js R static/scripts/utils/add-logging.js R static/scripts/utils/ajax-queue.js R static/scripts/utils/async-save-text.js R static/scripts/utils/config.js R static/scripts/utils/deferred.js R static/scripts/utils/graph.js R static/scripts/utils/levenshtein.js R static/scripts/utils/localization.js R static/scripts/utils/metrics-logger.js R static/scripts/utils/natural-sort.js R static/scripts/utils/query-string-parsing.js R static/scripts/utils/uploadbox.js R static/scripts/utils/utils.js R static/scripts/viz/bbi-data-manager.js R static/scripts/viz/circster.js R static/scripts/viz/phyloviz.js R static/scripts/viz/sweepster.js R static/scripts/viz/trackster.js R static/scripts/viz/trackster/filters.js R static/scripts/viz/trackster/painters.js R static/scripts/viz/trackster/slotting.js R static/scripts/viz/trackster/tracks.js R static/scripts/viz/trackster/util.js R static/scripts/viz/visualization.js R static/scripts/viz/viz_views.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/circster.css M static/style/blue/embed_item.css M static/style/blue/library.css M static/style/blue/reports.css M static/style/blue/trackster.css M static/welcome.html.sample R templates/admin/impersonate.mako R templates/admin/view_data_tables_registry.mako R templates/admin/view_datatypes_registry.mako M templates/base/base_panels.mako M templates/display_common.mako M templates/ind_share_base.mako M templates/js-app.mako R templates/sharing_base.mako M templates/show_params.mako M templates/tagging_common.mako M templates/user/login.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/structure.mako R templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako A test-data/1.csv A test-data/1.tiff A test-data/11.tabular A test-data/configfile.json A test-data/example-bag.zip A test-data/filter1_in6.bed A test-data/filter1_test6.bed A test-data/new_tags_1.txt A test-data/qname_sorted.bam A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/treated1fb.txt A test-data/rules/treated2fb.txt A test-data/rules/treated3fb.txt A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv A test-data/rules/untreated1fb.txt A test-data/rules/untreated2fb.txt A test-data/rules/untreated3fb.txt A test-data/rules/untreated4fb.txt A test-data/sort_out1.bed A test-data/sort_out2.bed A test-data/sort_out3.tab A test-data/sort_out4.sam A test-data/testdir1.zip M test/api/test_dataset_collections.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_visualizations.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/api.py A test/base/data/rules_dsl_spec.yml M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/populators.py A test/base/rules_test_data.py M test/base/testcase.py R test/base/tool_shed_util.py A test/base/workflow_fixtures.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py R test/casperjs/README.txt R test/casperjs/api-anon-history-permission-tests.js R test/casperjs/api-anon-history-tests.js R test/casperjs/api-hda-tests.js R test/casperjs/api-history-permission-tests.js R test/casperjs/casperjs_runner.py R test/casperjs/modules/api.js R test/casperjs/modules/historyoptions.js R test/casperjs/modules/historypanel.js R test/casperjs/modules/tools.js R test/casperjs/modules/user.js R test/casperjs/page-data/selectors.json R test/casperjs/server_env.py R test/casperjs/spaceghost.js R test/casperjs/test-data/simple_test.ga R test/casperjs/utils/simple-galaxy.js M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh M test/functional/test_data_managers.py M test/functional/test_toolbox.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml A test/functional/tools/collection_type_source_map_over.xml A test/functional/tools/column_param_configfile.xml A test/functional/tools/empty_select.xml A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/for_workflows/cat_collection.xml A test/functional/tools/identifier_single_in_repeat.xml A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/job_properties.xml M test/functional/tools/multi_data_optional.xml M test/functional/tools/multi_output_recurse.xml A test/functional/tools/output_action_change_format_paired.xml R test/functional/tools/paired_collection_map_over_structured_like.xml R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/twilltestcase.py M test/galaxy_selenium/components.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/integration/test_data_manager_table_reload.py A test/integration/test_scripts.py A test/integration/test_shed_tool_tests.py M test/integration/test_upload_configuration_options.py A test/integration/uses_shed.py R test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py A test/selenium_tests/test_admin_app.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/test_bam.py A test/unit/datatypes/test_datatypes_registry.py A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_params.py M test/unit/managers/test_HistoryManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_remote_shell.py A test/unit/test_rule_utils.py M test/unit/test_security_helper.py A test/unit/test_security_passwords.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_validation.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py A tool-data/intermine_simple_display.loc.sample A tools/data_source/intermine.xml M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/codingSnps.xml M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/bed_to_bigbed.xml M tools/filters/cutWrapper.pl M tools/filters/sorter.py M tools/filters/sorter.xml M tools/filters/wig_to_bigwig.xml M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.py M tools/stats/filtering.xml M tox.ini
Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into select_tag_parameter
Commit: d417e9b239309707274011d4199b8f827fcc0f6d https://github.com/galaxyproject/galaxy/commit/d417e9b239309707274011d4199b8... Author: John Chilton jmchilton@gmail.com Date: 2018-07-24 (Tue, 24 Jul 2018)
Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_cat_group_tag.xml A test/functional/tools/collection_cat_group_tag_multiple.xml M test/functional/tools/samples_tool_conf.xml
Log Message: ----------- Flush out collection tag parameters a bit.
- Switch select_tag to group_tag as a parameter name - since it is restricted to group_tags and we don't call data parameters select_data. - Add minimal XSD documentation for this new parameter type. - Add example tools - for single and multiple tags. - Add API tests for these tools and the tag handling.
Commit: e5c532298d5db34da04d8f046ebe44abddbbaa64 https://github.com/galaxyproject/galaxy/commit/e5c532298d5db34da04d8f046ebe4... Author: John Chilton jmchilton@gmail.com Date: 2018-07-25 (Wed, 25 Jul 2018)
Changed paths: M lib/galaxy/tools/parameters/basic.py
Log Message: ----------- Make tag order stable when using group_tag parameters.
Commit: 6677e7b91385d027989613bdc621108da76e8425 https://github.com/galaxyproject/galaxy/commit/6677e7b91385d027989613bdc6211... Author: John Chilton jmchilton@gmail.com Date: 2018-07-25 (Wed, 25 Jul 2018)
Changed paths: M lib/galaxy/tools/wrappers.py
Log Message: ----------- Fix failing import/export test for group_tag changes.
Commit: 5a914b9fa71ff2c00d7ba1a7c1dc3ccbb8437eae https://github.com/galaxyproject/galaxy/commit/5a914b9fa71ff2c00d7ba1a7c1dc3... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-08-07 (Tue, 07 Aug 2018)
Changed paths: M lib/galaxy/tools/parameters/basic.py
Log Message: ----------- Keep all user-selected tags, including duplicates
Commit: 95e8a3491280cc26d435bebc1cf03488d7db3b88 https://github.com/galaxyproject/galaxy/commit/95e8a3491280cc26d435bebc1cf03... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-08-07 (Tue, 07 Aug 2018)
Changed paths: M lib/galaxy/tools/parameters/basic.py
Log Message: ----------- Correct copy-pasted docstring
Commit: 55436c38008c3d1b261b7d9dfc728cc968bd6622 https://github.com/galaxyproject/galaxy/commit/55436c38008c3d1b261b7d9dfc728... Author: John Chilton jmchilton@gmail.com Date: 2018-08-07 (Tue, 07 Aug 2018)
Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_cat_group_tag.xml A test/functional/tools/collection_cat_group_tag_multiple.xml M test/functional/tools/samples_tool_conf.xml M test/unit/test_objectstore.py M test/unit/tools/test_wrappers.py
Log Message: ----------- Merge pull request #5457 from mvdbeek/select_tag_parameter
Allow selecting subset of collection by group tag
Compare: https://github.com/galaxyproject/galaxy/compare/d1423b6e18cb...55436c38008c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.