[galaxy-commits] [galaxyproject/galaxy] 458766: Add run workflow tool form

14 Dec 2015


      Branch: refs/heads/dev
  Home:   https://github.com/galaxyproject/galaxy
  Commit: 458766b00f05a2d46c834d461e59201796ff0358
      https://github.com/galaxyproject/galaxy/commit/458766b00f05a2d46c834d461e592...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-11-20 (Fri, 20 Nov 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/app/app-analysis.js
    M client/galaxy/scripts/mvc/dataset/dataset-li-edit.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-repeat.js
    M client/galaxy/scripts/mvc/form/form-section.js
    M client/galaxy/scripts/mvc/form/form-select-content.js
    M client/galaxy/scripts/mvc/form/form-view.js
    A client/galaxy/scripts/mvc/tool/tool-form-base.js
    A client/galaxy/scripts/mvc/tool/tool-form-composite.js
    A client/galaxy/scripts/mvc/tool/tool-form-workflow.js
    A client/galaxy/scripts/mvc/tool/tool-form.js
    A client/galaxy/scripts/mvc/tool/tool-template.js
    M client/galaxy/scripts/mvc/tools.js
    R client/galaxy/scripts/mvc/tools/tools-form-base.js
    R client/galaxy/scripts/mvc/tools/tools-form-workflow.js
    R client/galaxy/scripts/mvc/tools/tools-form.js
    R client/galaxy/scripts/mvc/tools/tools-jobs.js
    R client/galaxy/scripts/mvc/tools/tools-template.js
    M client/galaxy/scripts/mvc/ui/ui-misc.js
    M client/galaxy/scripts/mvc/ui/ui-portlet.js
    M client/galaxy/scripts/mvc/ui/ui-slider.js
    M client/galaxy/scripts/mvc/workflow/workflow-view.js
    M client/galaxy/scripts/utils/utils.js
    M client/galaxy/style/less/galaxy_bootstrap/variables.less
    M client/galaxy/style/less/ui.less
    M lib/galaxy/tools/__init__.py
    M lib/galaxy/tools/parameters/basic.py
    M lib/galaxy/webapps/galaxy/api/workflows.py
    M static/maps/galaxy-app-base.js.map
    M static/maps/mvc/app/app-analysis.js.map
    M static/maps/mvc/dataset/dataset-li-edit.js.map
    M static/maps/mvc/form/form-data.js.map
    M static/maps/mvc/form/form-input.js.map
    M static/maps/mvc/form/form-parameters.js.map
    M static/maps/mvc/form/form-repeat.js.map
    M static/maps/mvc/form/form-section.js.map
    M static/maps/mvc/form/form-select-content.js.map
    M static/maps/mvc/form/form-view.js.map
    A static/maps/mvc/tool/tool-form-base.js.map
    A static/maps/mvc/tool/tool-form-composite.js.map
    A static/maps/mvc/tool/tool-form-workflow.js.map
    A static/maps/mvc/tool/tool-form.js.map
    A static/maps/mvc/tool/tool-template.js.map
    M static/maps/mvc/tools.js.map
    R static/maps/mvc/tools/tools-form-base.js.map
    R static/maps/mvc/tools/tools-form-workflow.js.map
    R static/maps/mvc/tools/tools-form.js.map
    R static/maps/mvc/tools/tools-jobs.js.map
    R static/maps/mvc/tools/tools-template.js.map
    M static/maps/mvc/ui/ui-misc.js.map
    M static/maps/mvc/ui/ui-portlet.js.map
    M static/maps/mvc/ui/ui-slider.js.map
    M static/maps/mvc/workflow/workflow-view.js.map
    M static/maps/utils/utils.js.map
    M static/scripts/mvc/app/app-analysis.js
    M static/scripts/mvc/dataset/dataset-li-edit.js
    M static/scripts/mvc/form/form-data.js
    M static/scripts/mvc/form/form-input.js
    M static/scripts/mvc/form/form-parameters.js
    M static/scripts/mvc/form/form-repeat.js
    M static/scripts/mvc/form/form-section.js
    M static/scripts/mvc/form/form-select-content.js
    M static/scripts/mvc/form/form-view.js
    A static/scripts/mvc/tool/tool-form-base.js
    A static/scripts/mvc/tool/tool-form-composite.js
    A static/scripts/mvc/tool/tool-form-workflow.js
    A static/scripts/mvc/tool/tool-form.js
    A static/scripts/mvc/tool/tool-template.js
    M static/scripts/mvc/tools.js
    R static/scripts/mvc/tools/tools-form-base.js
    R static/scripts/mvc/tools/tools-form-workflow.js
    R static/scripts/mvc/tools/tools-form.js
    R static/scripts/mvc/tools/tools-jobs.js
    R static/scripts/mvc/tools/tools-template.js
    M static/scripts/mvc/ui/ui-misc.js
    M static/scripts/mvc/ui/ui-portlet.js
    M static/scripts/mvc/ui/ui-slider.js
    M static/scripts/mvc/workflow/workflow-view.js
    M static/scripts/utils/utils.js
    M static/style/blue/base.css
    M templates/webapps/galaxy/workflow/run.mako

  Log Message:
  -----------
  Add run workflow tool form

Move styles to css

Improve handling of numeric workflow parameters


  Commit: 9f7dff740f0133d6ba66abe067fb2edeb7a6b705
      https://github.com/galaxyproject/galaxy/commit/9f7dff740f0133d6ba66abe067fb2...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-11-20 (Fri, 20 Nov 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
    M static/maps/mvc/tool/tool-form-workflow.js.map
    M static/scripts/mvc/tool/tool-form-workflow.js

  Log Message:
  -----------
  Revise is_workflow setting


  Commit: 0770d8d988b20e36c2178d906bd05c6471018edf
      https://github.com/galaxyproject/galaxy/commit/0770d8d988b20e36c2178d906bd05...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-11-20 (Fri, 20 Nov 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/tool/tool-form-base.js
    M lib/galaxy/tools/__init__.py
    M lib/galaxy/tools/parameters/basic.py
    M lib/galaxy/webapps/galaxy/api/workflows.py
    M static/maps/mvc/tool/tool-form-base.js.map
    M static/scripts/mvc/tool/tool-form-base.js
    M templates/webapps/galaxy/workflow/editor_tool_form.mako
    M templates/webapps/galaxy/workflow/run.mako

  Log Message:
  -----------
  Revise workflow mode flag handling

Fix comment


  Commit: 28715a5bca299933c69859559d5b88b381b6c998
      https://github.com/galaxyproject/galaxy/commit/28715a5bca299933c69859559d5b8...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-01 (Tue, 01 Dec 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/form/form-input.js
    M client/galaxy/scripts/mvc/form/form-section.js
    M client/galaxy/scripts/mvc/tool/tool-form-composite.js
    M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
    M client/galaxy/style/less/ui.less
    M lib/galaxy/tools/__init__.py
    M static/maps/mvc/form/form-input.js.map
    M static/maps/mvc/form/form-section.js.map
    M static/maps/mvc/tool/tool-form-composite.js.map
    M static/maps/mvc/tool/tool-form-workflow.js.map
    M static/scripts/mvc/form/form-input.js
    M static/scripts/mvc/form/form-section.js
    M static/scripts/mvc/tool/tool-form-composite.js
    M static/style/blue/base.css

  Log Message:
  -----------
  Add runtime modification switch


  Commit: 2f31a3cbcd087f26caa9b8754920a6dddb924b30
      https://github.com/galaxyproject/galaxy/commit/2f31a3cbcd087f26caa9b8754920a...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-01 (Tue, 01 Dec 2015)

  Changed paths:
    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/tool/tool-form-composite.js
    M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
    M static/maps/mvc/form/form-input.js.map
    M static/maps/mvc/form/form-parameters.js.map
    M static/maps/mvc/form/form-section.js.map
    M static/maps/mvc/tool/tool-form-composite.js.map
    M static/maps/mvc/tool/tool-form-workflow.js.map
    M static/scripts/mvc/form/form-input.js
    M static/scripts/mvc/form/form-parameters.js
    M static/scripts/mvc/form/form-section.js
    M static/scripts/mvc/tool/tool-form-composite.js
    M static/scripts/mvc/tool/tool-form-workflow.js

  Log Message:
  -----------
  Cleanup collapsible handling


  Commit: 3017c61f380c8caa722ff04d11e2e3d37ca56b1c
      https://github.com/galaxyproject/galaxy/commit/3017c61f380c8caa722ff04d11e2e...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-01 (Tue, 01 Dec 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/tool/tool-form-composite.js
    M static/maps/mvc/tool/tool-form-composite.js.map
    M static/scripts/mvc/tool/tool-form-composite.js

  Log Message:
  -----------
  Fix step order


  Commit: 98e738d6f0cb2faae1c304a889baaa66b10df953
      https://github.com/galaxyproject/galaxy/commit/98e738d6f0cb2faae1c304a889baa...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-01 (Tue, 01 Dec 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/tool/tool-form-composite.js
    M static/maps/mvc/tool/tool-form-composite.js.map
    M static/scripts/mvc/tool/tool-form-composite.js

  Log Message:
  -----------
  Show pja info inside form portlet

Improve readability


  Commit: aa90e346dd4e10850482e38c7331864bef50f007
      https://github.com/galaxyproject/galaxy/commit/aa90e346dd4e10850482e38c73318...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-02 (Wed, 02 Dec 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/form/form-view.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-workflow.js
    M client/galaxy/scripts/mvc/tool/tool-form.js
    M lib/galaxy/tools/parameters/basic.py
    M static/maps/mvc/form/form-view.js.map
    M static/maps/mvc/tool/tool-form-base.js.map
    M static/maps/mvc/tool/tool-form-composite.js.map
    M static/maps/mvc/tool/tool-form-workflow.js.map
    M static/maps/mvc/tool/tool-form.js.map
    M static/scripts/mvc/form/form-view.js
    M static/scripts/mvc/tool/tool-form-base.js
    M static/scripts/mvc/tool/tool-form-composite.js
    M static/scripts/mvc/tool/tool-form-workflow.js
    M static/scripts/mvc/tool/tool-form.js

  Log Message:
  -----------
  Revise form base

Fix style


  Commit: a8a4480d5c7e92e0f121eefd66357f5504c4cb26
      https://github.com/galaxyproject/galaxy/commit/a8a4480d5c7e92e0f121eefd66357...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-03 (Thu, 03 Dec 2015)

  Changed paths:
    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-repeat.js
    M client/galaxy/scripts/mvc/form/form-section.js
    M client/galaxy/scripts/mvc/form/form-select-content.js
    M client/galaxy/scripts/mvc/form/form-view.js
    M client/galaxy/scripts/mvc/tool/tool-form-base.js
    M client/galaxy/scripts/mvc/tool/tool-form-composite.js
    M client/galaxy/style/less/ui.less
    M config/plugins/visualizations/charts/static/build-app.js
    M config/plugins/visualizations/charts/static/library/ui-table-form.js
    M config/plugins/visualizations/charts/static/views/editor.js
    M lib/galaxy/tools/__init__.py
    M lib/galaxy/tools/parameters/dataset_matcher.py
    M static/maps/mvc/form/form-data.js.map
    M static/maps/mvc/form/form-input.js.map
    M static/maps/mvc/form/form-repeat.js.map
    M static/maps/mvc/form/form-section.js.map
    M static/maps/mvc/form/form-select-content.js.map
    M static/maps/mvc/form/form-view.js.map
    M static/maps/mvc/tool/tool-form-base.js.map
    M static/maps/mvc/tool/tool-form-composite.js.map
    M static/scripts/mvc/form/form-input.js
    M static/scripts/mvc/form/form-repeat.js
    M static/scripts/mvc/form/form-section.js
    M static/scripts/mvc/form/form-select-content.js
    M static/scripts/mvc/form/form-view.js
    M static/scripts/mvc/tool/tool-form-base.js
    M static/scripts/mvc/tool/tool-form-composite.js
    M static/style/blue/base.css
    M templates/webapps/galaxy/workflow/run.mako

  Log Message:
  -----------
  Fix dataset matching


  Commit: ac79cf191c0a0588cdaf45b5075a2494bf097f57
      https://github.com/galaxyproject/galaxy/commit/ac79cf191c0a0588cdaf45b5075a2...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-03 (Thu, 03 Dec 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/form/form-input.js
    M client/galaxy/style/less/ui.less
    M static/maps/mvc/form/form-input.js.map
    M static/scripts/mvc/form/form-input.js
    M static/style/blue/base.css

  Log Message:
  -----------
  Fix style naming


  Commit: 4dc134d43bfa415cf3d1b77475dc0d4a3efb05b1
      https://github.com/galaxyproject/galaxy/commit/4dc134d43bfa415cf3d1b77475dc0...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-05 (Sat, 05 Dec 2015)

  Changed paths:
    M .gitignore
    M README.rst
    M client/GruntFile.js
    A client/galaxy/scripts/apps/analysis.js
    A client/galaxy/scripts/apps/history-panel.js
    A client/galaxy/scripts/apps/login.js
    A client/galaxy/scripts/apps/tool-panel.js
    R client/galaxy/scripts/base.js
    R client/galaxy/scripts/galaxy-app-base.js
    R client/galaxy/scripts/galaxy.autocom_tagging.js
    R client/galaxy/scripts/galaxy.base.js
    R client/galaxy/scripts/galaxy.frame.js
    A client/galaxy/scripts/galaxy.js
    M client/galaxy/scripts/galaxy.library.js
    R client/galaxy/scripts/galaxy.masthead.js
    R client/galaxy/scripts/galaxy.menu.js
    M client/galaxy/scripts/galaxy.pages.js
    R client/galaxy/scripts/galaxy.panels.js
    R client/galaxy/scripts/galaxy.tools.js
    R client/galaxy/scripts/galaxy.ui.scrollPanel.js
    A client/galaxy/scripts/layout/masthead.js
    A client/galaxy/scripts/layout/menu.js
    A client/galaxy/scripts/layout/modal.js
    A client/galaxy/scripts/layout/page.js
    A client/galaxy/scripts/layout/panel.js
    A client/galaxy/scripts/layout/scratchbook.js
    R client/galaxy/scripts/libs/IE/IE7.js
    R client/galaxy/scripts/libs/IE/IE8.js
    R client/galaxy/scripts/libs/IE/blank.gif
    R client/galaxy/scripts/libs/IE/excanvas.js
    R client/galaxy/scripts/libs/IE/ie7-recalc.js
    A client/galaxy/scripts/libs/backbone.js
    R client/galaxy/scripts/libs/backbone/backbone.js
    M client/galaxy/scripts/libs/d3.js
    A client/galaxy/scripts/mvc/annotation.js
    R client/galaxy/scripts/mvc/annotations.js
    R client/galaxy/scripts/mvc/app/app-login.js
    R client/galaxy/scripts/mvc/app/app-view.js
    M client/galaxy/scripts/mvc/base-mvc.js
    M client/galaxy/scripts/mvc/citation/citation-model.js
    M client/galaxy/scripts/mvc/collection/collection-model.js
    R client/galaxy/scripts/mvc/collection/collection-panel-edit.js
    R client/galaxy/scripts/mvc/collection/collection-panel.js
    A client/galaxy/scripts/mvc/collection/collection-view-edit.js
    A 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
    R client/galaxy/scripts/mvc/data.js
    A client/galaxy/scripts/mvc/dataset/data.js
    M client/galaxy/scripts/mvc/dataset/dataset-choice.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-list.js
    M client/galaxy/scripts/mvc/dataset/dataset-model.js
    M client/galaxy/scripts/mvc/form/form-select-content.js
    M client/galaxy/scripts/mvc/grid/grid-view.js
    M client/galaxy/scripts/mvc/history/copy-dialog.js
    M client/galaxy/scripts/mvc/history/hda-model.js
    M client/galaxy/scripts/mvc/history/hdca-li-edit.js
    M client/galaxy/scripts/mvc/history/hdca-li.js
    M client/galaxy/scripts/mvc/history/history-content-model.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/history-model.js
    R client/galaxy/scripts/mvc/history/history-panel-annotated.js
    R client/galaxy/scripts/mvc/history/history-panel-edit-current.js
    R client/galaxy/scripts/mvc/history/history-panel-edit.js
    R client/galaxy/scripts/mvc/history/history-panel.js
    A client/galaxy/scripts/mvc/history/history-view-annotated.js
    A client/galaxy/scripts/mvc/history/history-view-edit-current.js
    A client/galaxy/scripts/mvc/history/history-view-edit.js
    A client/galaxy/scripts/mvc/history/history-view.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/scripts/mvc/history/options-menu.js
    M client/galaxy/scripts/mvc/job/job-li.js
    M client/galaxy/scripts/mvc/job/job-model.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/library/library-model.js
    R client/galaxy/scripts/mvc/list/list-panel.js
    A client/galaxy/scripts/mvc/list/list-view.js
    A client/galaxy/scripts/mvc/tag.js
    R client/galaxy/scripts/mvc/tags.js
    A client/galaxy/scripts/mvc/tool/tools-form-base.js
    A client/galaxy/scripts/mvc/tool/tools-form-workflow.js
    A client/galaxy/scripts/mvc/tool/tools-form.js
    A client/galaxy/scripts/mvc/tool/tools-jobs.js
    A client/galaxy/scripts/mvc/tool/tools-template.js
    A client/galaxy/scripts/mvc/tool/tools.js
    R client/galaxy/scripts/mvc/tools.js
    M client/galaxy/scripts/mvc/ui/ui-buttons.js
    M client/galaxy/scripts/mvc/ui/ui-select-default.js
    M client/galaxy/scripts/mvc/ui/ui-select-ftp.js
    M client/galaxy/scripts/mvc/ui/ui-select-library.js
    M client/galaxy/scripts/mvc/upload/upload-ftp.js
    M client/galaxy/scripts/mvc/upload/upload-view.js
    M client/galaxy/scripts/mvc/user/user-model.js
    M client/galaxy/scripts/mvc/visualization/visualization-model.js
    M client/galaxy/scripts/mvc/workflow/workflow-connector.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-view-data.js
    M client/galaxy/scripts/mvc/workflow/workflow-view.js
    M client/galaxy/scripts/nls/ja/locale.js
    M client/galaxy/scripts/nls/locale.js
    M client/galaxy/scripts/nls/zh/locale.js
    A client/galaxy/scripts/onload.js
    A client/galaxy/scripts/polyfills.js
    R client/galaxy/scripts/rgenetics/checkbox_and_radiobutton.js
    R client/galaxy/scripts/rgenetics/helper_functions.js
    R client/galaxy/scripts/rgenetics/timer.js
    M client/galaxy/scripts/templates/compiled/panel_section.js
    M client/galaxy/scripts/templates/compiled/tool_form.js
    M client/galaxy/scripts/templates/compiled/tool_link.js
    M client/galaxy/scripts/templates/compiled/tool_search.js
    R client/galaxy/scripts/tools/rgenetics/checkbox_and_radiobutton.js
    R client/galaxy/scripts/tools/rgenetics/helper_functions.js
    R client/galaxy/scripts/tools/rgenetics/timer.js
    A client/galaxy/scripts/ui/autocom_tagging.js
    A client/galaxy/scripts/ui/editable-text.js
    A client/galaxy/scripts/ui/popupmenu.js
    A client/galaxy/scripts/ui/scroll-panel.js
    A client/galaxy/scripts/utils/async-save-text.js
    M client/galaxy/scripts/utils/localization.js
    M client/galaxy/scripts/utils/query-string-parsing.js
    M client/galaxy/scripts/utils/utils.js
    M client/galaxy/scripts/viz/circster.js
    M client/galaxy/scripts/viz/phyloviz.js
    M client/galaxy/scripts/viz/sweepster.js
    M client/galaxy/scripts/viz/trackster.js
    M client/galaxy/scripts/viz/trackster/tracks.js
    M client/galaxy/scripts/viz/trackster/util.js
    M client/galaxy/scripts/viz/visualization.js
    M client/galaxy/style/less/base.less
    M client/grunt-tasks/install-libs.js
    M client/grunt-tasks/scripts.js
    M client/grunt-tasks/style.js
    M client/grunt-tasks/templates.js
    M client/package.json
    M client/toolshed/scripts/mvc/groups/group-detail-view.js
    M client/toolshed/scripts/mvc/groups/group-listrow-view.js
    A client/webpack.config.js
    M config/datatypes_conf.xml.sample
    A config/dependency_resolvers_conf.xml.sample
    M config/galaxy.ini.sample
    A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample
    A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml
    A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
    A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
    M config/plugins/interactive_environments/common/templates/ie.mako
    M config/plugins/interactive_environments/ipython/config/ipython.ini.sample
    M config/plugins/interactive_environments/ipython/static/js/ipython.js
    M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
    M config/plugins/visualizations/charts/templates/charts.mako
    A config/reports.ini.sample
    R config/reports_wsgi.ini.sample
    M config/tool_shed.ini.sample
    M doc/source/admin/interactive_environments.rst
    A doc/source/releases/15.10.rst
    M doc/source/releases/15.10_announce.rst
    A doc/source/releases/16.01_announce.rst
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    M lib/galaxy/datatypes/binary.py
    M lib/galaxy/datatypes/data.py
    M lib/galaxy/datatypes/graph.py
    M lib/galaxy/datatypes/interval.py
    M lib/galaxy/datatypes/proteomics.py
    M lib/galaxy/datatypes/registry.py
    M lib/galaxy/datatypes/sniff.py
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    A lib/galaxy/datatypes/test/test.mz5
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    A lib/galaxy/datatypes/triples.py
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    M lib/galaxy/jobs/output_checker.py
    M lib/galaxy/jobs/runners/__init__.py
    M lib/galaxy/jobs/runners/pulsar.py
    M lib/galaxy/managers/collections.py
    M lib/galaxy/managers/configuration.py
    M lib/galaxy/managers/users.py
    M lib/galaxy/managers/workflows.py
    M lib/galaxy/model/__init__.py
    M lib/galaxy/model/mapping.py
    M lib/galaxy/security/__init__.py
    M lib/galaxy/tools/__init__.py
    M lib/galaxy/tools/actions/__init__.py
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    M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
    M lib/galaxy/tools/evaluation.py
    M lib/galaxy/tools/execute.py
    M lib/galaxy/tools/parameters/basic.py
    M lib/galaxy/tools/parameters/wrapped.py
    M lib/galaxy/tools/parser/xml.py
    M lib/galaxy/tools/test.py
    M lib/galaxy/tools/wrappers.py
    M lib/galaxy/util/xml_macros.py
    M lib/galaxy/web/base/controller.py
    M lib/galaxy/web/base/controllers/admin.py
    M lib/galaxy/web/base/interactive_environments.py
    M lib/galaxy/web/framework/webapp.py
    M lib/galaxy/webapps/galaxy/api/workflows.py
    M lib/galaxy/webapps/galaxy/buildapp.py
    M lib/galaxy/webapps/galaxy/controllers/admin.py
    M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
    M lib/galaxy/webapps/galaxy/controllers/dataset.py
    M lib/galaxy/webapps/galaxy/controllers/external_service.py
    M lib/galaxy/webapps/galaxy/controllers/forms.py
    M lib/galaxy/webapps/galaxy/controllers/history.py
    M lib/galaxy/webapps/galaxy/controllers/library.py
    M lib/galaxy/webapps/galaxy/controllers/library_admin.py
    M lib/galaxy/webapps/galaxy/controllers/request_type.py
    M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
    M lib/galaxy/webapps/galaxy/controllers/requests_common.py
    M lib/galaxy/webapps/galaxy/controllers/root.py
    M lib/galaxy/webapps/galaxy/controllers/visualization.py
    M lib/galaxy/webapps/galaxy/controllers/workflow.py
    M lib/galaxy/webapps/reports/controllers/jobs.py
    M lib/galaxy/webapps/reports/controllers/sample_tracking.py
    M lib/galaxy/webapps/reports/controllers/workflows.py
    M lib/galaxy/webapps/tool_shed/api/repositories.py
    M lib/galaxy/webapps/tool_shed/config.py
    M lib/galaxy/webapps/tool_shed/controllers/repository.py
    M lib/galaxy/workflow/extract.py
    M lib/galaxy/workflow/modules.py
    M lib/galaxy/workflow/run.py
    M lib/galaxy/workflow/run_request.py
    M lib/tool_shed/galaxy_install/migrate/check.py
    M lib/tool_shed/grids/admin_grids.py
    M lib/tool_shed/grids/repository_grids.py
    M lib/tool_shed/grids/repository_review_grids.py
    M lib/tool_shed/util/common_util.py
    M lib/tool_shed/util/hg_util.py
    M lib/tool_shed/util/shed_util_common.py
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    M run_tests.sh
    M scripts/bootstrap_history.py
    M scripts/functional_tests.py
    M scripts/sync_reports_config.py
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    R static/maps/galaxy.autocom_tagging.js.map
    R static/maps/galaxy.base.js.map
    R static/maps/galaxy.frame.js.map
    A static/maps/galaxy.js.map
    M static/maps/galaxy.library.js.map
    R static/maps/galaxy.masthead.js.map
    R static/maps/galaxy.menu.js.map
    M static/maps/galaxy.pages.js.map
    R static/maps/galaxy.panels.js.map
    R static/maps/galaxy.tools.js.map
    R static/maps/galaxy.ui.scrollPanel.js.map
    R static/maps/galaxy.workflows.js.map
    A static/maps/layout/masthead.js.map
    A static/maps/layout/menu.js.map
    A static/maps/layout/modal.js.map
    A static/maps/layout/page.js.map
    A static/maps/layout/panel.js.map
    A static/maps/layout/scratchbook.js.map
    R static/maps/libs/IE/IE7.js.map
    R static/maps/libs/IE/IE8.js.map
    R static/maps/libs/IE/excanvas.js.map
    R static/maps/libs/IE/ie7-recalc.js.map
    A static/maps/libs/backbone.js.map
    A static/maps/libs/common-libs.js.map
    A static/maps/mvc/annotation.js.map
    R static/maps/mvc/annotations.js.map
    R static/maps/mvc/app/app-login.js.map
    R static/maps/mvc/app/app-view.js.map
    M static/maps/mvc/base-mvc.js.map
    M static/maps/mvc/citation/citation-model.js.map
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    M static/maps/mvc/history/options-menu.js.map
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    M static/maps/mvc/library/library-dataset-view.js.map
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    M static/maps/mvc/library/library-folderrow-view.js.map
    M static/maps/mvc/library/library-foldertoolbar-view.js.map
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    A static/maps/mvc/tool/tools-form-base.js.map
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    A static/maps/mvc/tool/tools-form.js.map
    A static/maps/mvc/tool/tools-jobs.js.map
    A static/maps/mvc/tool/tools-template.js.map
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    M static/maps/mvc/upload/upload-view.js.map
    M static/maps/mvc/user/user-model.js.map
    M static/maps/mvc/visualization/visualization-model.js.map
    M static/maps/mvc/workflow/workflow-connector.js.map
    M static/maps/mvc/workflow/workflow-manager.js.map
    M static/maps/mvc/workflow/workflow-node.js.map
    M static/maps/mvc/workflow/workflow-view-data.js.map
    M static/maps/mvc/workflow/workflow-view.js.map
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    A static/maps/polyfills.js.map
    R static/maps/rgenetics/checkbox_and_radiobutton.js.map
    R static/maps/rgenetics/helper_functions.js.map
    R static/maps/rgenetics/timer.js.map
    M static/maps/templates/compiled/panel_section.js.map
    M static/maps/templates/compiled/tool_form.js.map
    M static/maps/templates/compiled/tool_link.js.map
    M static/maps/templates/compiled/tool_search.js.map
    R static/maps/tools/rgenetics/checkbox_and_radiobutton.js.map
    R static/maps/tools/rgenetics/helper_functions.js.map
    R static/maps/tools/rgenetics/timer.js.map
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    A static/maps/ui/editable-text.js.map
    A static/maps/ui/popupmenu.js.map
    A static/maps/ui/scroll-panel.js.map
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    M static/maps/utils/localization.js.map
    M static/maps/utils/query-string-parsing.js.map
    M static/maps/utils/utils.js.map
    M static/maps/viz/circster.js.map
    M static/maps/viz/phyloviz.js.map
    M static/maps/viz/sweepster.js.map
    M static/maps/viz/trackster.js.map
    M static/maps/viz/trackster/tracks.js.map
    M static/maps/viz/trackster/util.js.map
    M static/maps/viz/visualization.js.map
    R static/scripts/base.js
    A static/scripts/bundled/analysis.bundled.js
    A static/scripts/bundled/analysis.bundled.js.map
    A static/scripts/bundled/libs.bundled.js
    A static/scripts/bundled/libs.bundled.js.map
    A static/scripts/bundled/login.bundled.js
    A static/scripts/bundled/login.bundled.js.map
    R static/scripts/galaxy-app-base.js
    R static/scripts/galaxy.autocom_tagging.js
    R static/scripts/galaxy.base.js
    R static/scripts/galaxy.frame.js
    A static/scripts/galaxy.js
    M static/scripts/galaxy.library.js
    R static/scripts/galaxy.masthead.js
    R static/scripts/galaxy.menu.js
    M static/scripts/galaxy.pages.js
    R static/scripts/galaxy.panels.js
    R static/scripts/galaxy.tools.js
    R static/scripts/galaxy.ui.scrollPanel.js
    R static/scripts/galaxy.workflows.js
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    R static/scripts/libs/IE/IE8.js
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    R static/scripts/libs/IE/ie7-recalc.js
    A static/scripts/libs/backbone.js
    A static/scripts/libs/common-libs.js
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    R static/scripts/mvc/annotations.js
    R static/scripts/mvc/app/app-login.js
    R static/scripts/mvc/app/app-view.js
    M static/scripts/mvc/base-mvc.js
    M static/scripts/mvc/citation/citation-model.js
    M static/scripts/mvc/collection/collection-model.js
    R static/scripts/mvc/collection/collection-panel-edit.js
    R static/scripts/mvc/collection/collection-panel.js
    A static/scripts/mvc/collection/collection-view-edit.js
    A static/scripts/mvc/collection/collection-view.js
    M static/scripts/mvc/collection/list-collection-creator.js
    M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
    M static/scripts/mvc/collection/pair-collection-creator.js
    R static/scripts/mvc/data.js
    A static/scripts/mvc/dataset/data.js
    M static/scripts/mvc/dataset/dataset-choice.js
    M static/scripts/mvc/dataset/dataset-li-edit.js
    M static/scripts/mvc/dataset/dataset-li.js
    M static/scripts/mvc/dataset/dataset-list.js
    M static/scripts/mvc/dataset/dataset-model.js
    M static/scripts/mvc/form/form-select-content.js
    M static/scripts/mvc/history/copy-dialog.js
    M static/scripts/mvc/history/hdca-li-edit.js
    M static/scripts/mvc/history/hdca-li.js
    M static/scripts/mvc/history/history-content-model.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    R static/scripts/mvc/history/history-panel-annotated.js
    R static/scripts/mvc/history/history-panel-edit-current.js
    R static/scripts/mvc/history/history-panel-edit.js
    M static/scripts/mvc/history/history-panel.js
    A static/scripts/mvc/history/history-view-annotated.js
    A static/scripts/mvc/history/history-view-edit-current.js
    A static/scripts/mvc/history/history-view-edit.js
    A static/scripts/mvc/history/history-view.js
    M static/scripts/mvc/history/multi-panel.js
    M static/scripts/mvc/history/options-menu.js
    M static/scripts/mvc/job/job-li.js
    M static/scripts/mvc/job/job-model.js
    M static/scripts/mvc/library/library-dataset-view.js
    M static/scripts/mvc/library/library-folder-view.js
    M static/scripts/mvc/library/library-folderlist-view.js
    M static/scripts/mvc/library/library-folderrow-view.js
    M static/scripts/mvc/library/library-foldertoolbar-view.js
    M static/scripts/mvc/library/library-library-view.js
    M static/scripts/mvc/library/library-librarylist-view.js
    M static/scripts/mvc/library/library-libraryrow-view.js
    M static/scripts/mvc/library/library-librarytoolbar-view.js
    M static/scripts/mvc/library/library-model.js
    R static/scripts/mvc/list/list-panel.js
    A static/scripts/mvc/list/list-view.js
    A static/scripts/mvc/tag.js
    R static/scripts/mvc/tags.js
    A static/scripts/mvc/tool/tools-form-base.js
    A static/scripts/mvc/tool/tools-form-workflow.js
    A static/scripts/mvc/tool/tools-form.js
    A static/scripts/mvc/tool/tools-jobs.js
    A static/scripts/mvc/tool/tools-template.js
    A static/scripts/mvc/tool/tools.js
    A static/scripts/mvc/tools/tools-form-base.js
    M static/scripts/mvc/ui/ui-buttons.js
    M static/scripts/mvc/ui/ui-select-default.js
    M static/scripts/mvc/ui/ui-select-ftp.js
    M static/scripts/mvc/ui/ui-select-library.js
    M static/scripts/mvc/upload/upload-ftp.js
    M static/scripts/mvc/upload/upload-view.js
    M static/scripts/mvc/user/user-model.js
    M static/scripts/mvc/visualization/visualization-model.js
    M static/scripts/mvc/workflow/workflow-connector.js
    M static/scripts/mvc/workflow/workflow-manager.js
    M static/scripts/mvc/workflow/workflow-node.js
    M static/scripts/mvc/workflow/workflow-view-data.js
    M static/scripts/mvc/workflow/workflow-view.js
    A static/scripts/onload.js
    A static/scripts/polyfills.js
    R static/scripts/rgenetics/checkbox_and_radiobutton.js
    R static/scripts/rgenetics/helper_functions.js
    R static/scripts/rgenetics/timer.js
    M static/scripts/templates/compiled/panel_section.js
    M static/scripts/templates/compiled/tool_form.js
    M static/scripts/templates/compiled/tool_link.js
    M static/scripts/templates/compiled/tool_search.js
    R static/scripts/tools/rgenetics/checkbox_and_radiobutton.js
    R static/scripts/tools/rgenetics/helper_functions.js
    R static/scripts/tools/rgenetics/timer.js
    A static/scripts/ui/autocom_tagging.js
    A static/scripts/ui/editable-text.js
    A static/scripts/ui/popupmenu.js
    A static/scripts/ui/scroll-panel.js
    A static/scripts/utils/async-save-text.js
    M static/scripts/utils/localization.js
    M static/scripts/utils/query-string-parsing.js
    M static/scripts/utils/utils.js
    M static/scripts/viz/circster.js
    M static/scripts/viz/phyloviz.js
    M static/scripts/viz/sweepster.js
    M static/scripts/viz/trackster.js
    M static/scripts/viz/trackster/tracks.js
    M static/scripts/viz/trackster/util.js
    M static/scripts/viz/visualization.js
    M static/style/blue/autocomplete_tagging.css
    M static/style/blue/base.css
    M static/style/blue/embed_item.css
    R static/style/blue/galaxy.frame.masthead.css
    M static/style/blue/iphone.css
    M static/style/blue/library.css
    M static/style/blue/trackster.css
    M templates/base.mako
    M templates/base/base_panels.mako
    M templates/display_base.mako
    M templates/galaxy_client_app.mako
    M templates/grid_base.mako
    A templates/js-app.mako
    M templates/refresh_frames.mako
    M templates/tagging_common.mako
    M templates/user/logout.mako
    M templates/webapps/galaxy/dataset/display.mako
    M templates/webapps/galaxy/dataset/edit_attributes.mako
    M templates/webapps/galaxy/dataset/tabular_chunked.mako
    M templates/webapps/galaxy/galaxy.masthead.mako
    M templates/webapps/galaxy/galaxy.panels.mako
    M templates/webapps/galaxy/history/display.mako
    M templates/webapps/galaxy/history/embed.mako
    M templates/webapps/galaxy/history/view.mako
    M templates/webapps/galaxy/history/view_multiple.mako
    M templates/webapps/galaxy/library/common/ldda_edit_info.mako
    M templates/webapps/galaxy/library/common/move_library_item.mako
    M templates/webapps/galaxy/library/common/upload.mako
    M templates/webapps/galaxy/page/editor.mako
    M templates/webapps/galaxy/requests/common/create_request.mako
    M templates/webapps/galaxy/requests/common/find_samples.mako
    R templates/webapps/galaxy/root/index.mako
    M templates/webapps/galaxy/visualization/display.mako
    M templates/webapps/galaxy/visualization/display_in_frame.mako
    M templates/webapps/galaxy/visualization/sweepster.mako
    M templates/webapps/galaxy/workflow/editor.mako
    M templates/webapps/galaxy/workflow/run.mako
    M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako
    M test/api/helpers.py
    M test/api/test_jobs.py
    M test/api/test_tools.py
    M test/api/test_workflow_extraction.py
    M test/api/test_workflows.py
    M test/api/test_workflows_from_yaml.py
    A test/api/workflows_format_2/README.txt
    A test/api/workflows_format_2/__init__.py
    A test/api/workflows_format_2/converter.py
    A test/api/workflows_format_2/interface.py
    A test/api/workflows_format_2/main.py
    R test/api/yaml_to_workflow.py
    M test/base/twilltestcase.py
    M test/casperjs/api-history-permission-tests.js
    M test/casperjs/spaceghost.js
    A test/functional/tools/cheetah_problem_syntax_error.xml
    A test/functional/tools/cheetah_problem_unbound_var.xml
    A test/functional/tools/cheetah_problem_unbound_var_input.xml
    A test/functional/tools/collection_type_source.xml
    A test/functional/tools/create_10.xml
    A test/functional/tools/maxseconds.xml
    A test/functional/tools/output_format_collection.xml
    M test/functional/tools/samples_tool_conf.xml
    M test/functional/tools/simple_constructs.yml
    M test/qunit/package.json
    M test/qunit/test-app.js
    M test/qunit/test-common.js
    M test/qunit/test-data/bootstrapped.js
    M test/qunit/tests/galaxy-app-base.js
    M test/qunit/tests/workflow_editor_tests.js
    M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml
    M test/unit/test_galaxy_mapping.py
    M test/unit/tools/test_actions.py
    M test/unit/tools/test_data_parameters.py
    M test/unit/tools/test_parsing.py
    M test/unit/tools/test_tool_loader.py
    M test/unit/workflows/test_render.py
    A test/unit/workflows/test_workflow_progress.py
    M test/unit/workflows/workflow_support.py

  Log Message:
  -----------
  Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004


  Commit: 8e5b8016c6684e2364ba14b9061b0d5a2d218eb1
      https://github.com/galaxyproject/galaxy/commit/8e5b8016c6684e2364ba14b9061b0...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-05 (Sat, 05 Dec 2015)

  Changed paths:
    R client/galaxy/scripts/mvc/app/app-analysis.js
    R static/maps/mvc/app/app-analysis.js.map

  Log Message:
  -----------
  Remove files


  Commit: 7e5069baff533ba61fef3f8f6fc46ecab565a9c6
      https://github.com/galaxyproject/galaxy/commit/7e5069baff533ba61fef3f8f6fc46...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-05 (Sat, 05 Dec 2015)

  Changed paths:
    R client/galaxy/scripts/mvc/tool/tools-form-base.js
    R client/galaxy/scripts/mvc/tool/tools-form-workflow.js
    R client/galaxy/scripts/mvc/tool/tools-form.js
    R client/galaxy/scripts/mvc/tool/tools-jobs.js
    R client/galaxy/scripts/mvc/tool/tools-template.js
    R static/maps/mvc/tool/tools-form-base.js.map
    R static/maps/mvc/tool/tools-form-workflow.js.map
    R static/maps/mvc/tool/tools-form.js.map
    R static/maps/mvc/tool/tools-jobs.js.map
    R static/maps/mvc/tool/tools-template.js.map
    R static/maps/mvc/tools/tools-form-base.js.map
    R static/scripts/mvc/tool/tools-form-base.js
    R static/scripts/mvc/tool/tools-form-workflow.js
    R static/scripts/mvc/tool/tools-form.js
    R static/scripts/mvc/tool/tools-jobs.js
    R static/scripts/mvc/tool/tools-template.js
    R static/scripts/mvc/tools/tools-form-base.js

  Log Message:
  -----------
  Remove files


  Commit: 0f9cb1478f81d512d4232b42cf490b8022b3a420
      https://github.com/galaxyproject/galaxy/commit/0f9cb1478f81d512d4232b42cf490...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-05 (Sat, 05 Dec 2015)

  Changed paths:
    M static/style/blue/base.css

  Log Message:
  -----------
  Repack files


  Commit: e29f7155c479365ede4a69513e729fa1bc67c369
      https://github.com/galaxyproject/galaxy/commit/e29f7155c479365ede4a69513e729...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-05 (Sat, 05 Dec 2015)

  Changed paths:
    R static/maps/mvc/tools.js.map
    R static/scripts/mvc/app/app-analysis.js
    R static/scripts/mvc/tools.js

  Log Message:
  -----------
  Remove files


  Commit: 6820b29d3b867b452205c275f274449fb55c8119
      https://github.com/galaxyproject/galaxy/commit/6820b29d3b867b452205c275f2744...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-05 (Sat, 05 Dec 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/workflow/workflow-view.js
    M lib/galaxy/datatypes/constructive_solid_geometry.py
    M static/maps/mvc/workflow/workflow-view.js.map
    M static/scripts/mvc/workflow/workflow-view.js
    M test/api/helpers.py
    M test/functional/tools/maxseconds.xml

  Log Message:
  -----------
  Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004


  Commit: ab651fa89c0e24d637daa8bd5716b3932532c6a3
      https://github.com/galaxyproject/galaxy/commit/ab651fa89c0e24d637daa8bd5716b...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-06 (Sun, 06 Dec 2015)

  Changed paths:
    M client/galaxy/scripts/apps/analysis.js
    M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
    M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
    M client/galaxy/scripts/mvc/tool/tool-form.js
    M lib/galaxy/tools/__init__.py
    M lib/galaxy/tools/parameters/basic.py
    M static/maps/mvc/dataset/dataset-li-edit.js.map
    M static/maps/mvc/tool/tool-form-workflow.js.map
    M static/maps/mvc/tool/tool-form.js.map
    M static/maps/utils/utils.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/bundled/libs.bundled.js
    M static/scripts/bundled/libs.bundled.js.map
    M static/scripts/bundled/login.bundled.js
    M static/scripts/bundled/login.bundled.js.map
    M static/scripts/mvc/dataset/dataset-li-edit.js
    M static/scripts/mvc/tool/tool-form-workflow.js
    M static/scripts/mvc/tool/tool-form.js
    M static/scripts/utils/utils.js

  Log Message:
  -----------
  Fix url, lint and packing

Catch missing history, fix failing api test


  Commit: 00452e1b8aecd3ed2fc4c06262f451c9efafa1c6
      https://github.com/galaxyproject/galaxy/commit/00452e1b8aecd3ed2fc4c06262f45...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-06 (Sun, 06 Dec 2015)

  Changed paths:
    M lib/galaxy/tools/parameters/basic.py

  Log Message:
  -----------
  Add more specific error message for workflow parameters


  Commit: a951d34c703a239ac00c780025a9657bc7101b0b
      https://github.com/galaxyproject/galaxy/commit/a951d34c703a239ac00c780025a96...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-06 (Sun, 06 Dec 2015)

  Changed paths:
    M client/galaxy/scripts/apps/analysis.js
    M client/galaxy/scripts/apps/tool-panel.js
    M lib/galaxy/managers/configuration.py
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/bundled/libs.bundled.js.map

  Log Message:
  -----------
  Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004


  Commit: 8c6d530a661842a56fbb8800856237582701fc56
      https://github.com/galaxyproject/galaxy/commit/8c6d530a661842a56fbb880085623...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-07 (Mon, 07 Dec 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/tool/tool-form-base.js
    M lib/galaxy/managers/histories.py
    M lib/galaxy/managers/workflows.py
    M lib/galaxy/model/__init__.py
    M lib/galaxy/tools/__init__.py
    M lib/galaxy/tools/actions/__init__.py
    M lib/galaxy/tools/actions/upload.py
    M lib/galaxy/tools/execute.py
    M lib/galaxy/tools/toolbox/base.py
    M lib/galaxy/webapps/galaxy/api/users.py
    M lib/galaxy/workflow/modules.py
    M static/maps/mvc/tool/tool-form-base.js.map
    M static/scripts/mvc/tool/tool-form-base.js
    M templates/ind_share_base.mako
    M templates/webapps/galaxy/history/share.mako
    M test/unit/tools/test_execution.py

  Log Message:
  -----------
  Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004


  Commit: 485e8ef8f22330bce5a402c5b4bb0182ce5b180c
      https://github.com/galaxyproject/galaxy/commit/485e8ef8f22330bce5a402c5b4bb0...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-07 (Mon, 07 Dec 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/form/form-section.js
    M static/maps/mvc/form/form-section.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/bundled/libs.bundled.js.map
    M static/scripts/mvc/form/form-section.js

  Log Message:
  -----------
  Add fallback for missing section and repeat title


  Commit: 2b63427e965837eb29df54e5918cf8f84004f534
      https://github.com/galaxyproject/galaxy/commit/2b63427e965837eb29df54e5918cf...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-08 (Tue, 08 Dec 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/tool/tool-form-composite.js
    M lib/galaxy/managers/workflows.py
    M lib/galaxy/tools/__init__.py
    M lib/galaxy/tools/parameters/dynamic_options.py
    M static/maps/mvc/tool/tool-form-composite.js.map
    M static/scripts/mvc/tool/tool-form-composite.js

  Log Message:
  -----------
  Handle late validated dataset references


  Commit: 636e9900ba5e82c37a26fee84f56872c9413bd1b
      https://github.com/galaxyproject/galaxy/commit/636e9900ba5e82c37a26fee84f568...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-10 (Thu, 10 Dec 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/tool/tool-form-composite.js
    M static/maps/mvc/tool/tool-form-composite.js.map
    M static/scripts/mvc/tool/tool-form-composite.js

  Log Message:
  -----------
  Improve handling of unspecified workflow editor values


  Commit: 9a4c8343701c676ccf996cbbaa864f12135bac5b
      https://github.com/galaxyproject/galaxy/commit/9a4c8343701c676ccf996cbbaa864...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-10 (Thu, 10 Dec 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/ui/ui-drilldown.js
    M client/galaxy/style/less/ui.less
    M static/maps/mvc/ui/ui-drilldown.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/bundled/libs.bundled.js.map
    M static/scripts/mvc/ui/ui-drilldown.js
    M static/style/blue/base.css

  Log Message:
  -----------
  Use fa icons for drill down expansion


  Commit: c61a5529b4c788580d2c3615c7dab2386a9b8e4e
      https://github.com/galaxyproject/galaxy/commit/c61a5529b4c788580d2c3615c7dab...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-14 (Mon, 14 Dec 2015)

  Changed paths:
    A .ci/check_controller.sh
    A .ci/check_mako.sh
    A Makefile
    A client/.docker-build.sh
    A client/Dockerfile
    M client/galaxy/scripts/apps/analysis.js
    M client/galaxy/scripts/mvc/base-mvc.js
    M client/galaxy/scripts/mvc/citation/citation-model.js
    M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
    M client/galaxy/scripts/mvc/ui/ui-select-default.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-view-node.js
    M client/galaxy/scripts/mvc/workflow/workflow-view.js
    M client/galaxy/scripts/polyfills.js
    M client/galaxy/style/less/ui.less
    M config/dependency_resolvers_conf.xml.sample
    M config/reports.ini.sample
    M config/tool_shed.ini.sample
    A doc/source/admin/dependency_resolvers.rst
    M doc/source/admin/index.rst
    M doc/source/dev/faq.rst
    M lib/galaxy/datatypes/text.py
    M lib/galaxy/managers/base.py
    M lib/galaxy/managers/users.py
    M lib/galaxy/managers/workflows.py
    M lib/galaxy/model/tool_shed_install/__init__.py
    M lib/galaxy/tools/__init__.py
    M lib/galaxy/tools/deps/__init__.py
    M lib/galaxy/tools/deps/resolvers/modules.py
    M lib/galaxy/web/base/controller.py
    M lib/galaxy/webapps/galaxy/api/workflows.py
    M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
    M lib/galaxy/webapps/galaxy/controllers/root.py
    M lib/galaxy/webapps/galaxy/controllers/workflow.py
    M lib/galaxy/webapps/reports/config.py
    M lib/galaxy/webapps/tool_shed/config.py
    M lib/galaxy/webapps/tool_shed/model/__init__.py
    M lib/galaxy/workflow/modules.py
    M lib/galaxy/workflow/run.py
    M lib/tool_shed/galaxy_install/install_manager.py
    M lib/tool_shed/galaxy_install/migrate/check.py
    M lib/tool_shed/galaxy_install/repair_repository_manager.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
    M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
    M lib/tool_shed/util/tool_dependency_util.py
    M lib/tool_shed/util/workflow_util.py
    M run_tests.sh
    M static/maps/mvc/base-mvc.js.map
    M static/maps/mvc/citation/citation-model.js.map
    M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
    M static/maps/mvc/ui/ui-select-default.js.map
    M static/maps/mvc/workflow/workflow-manager.js.map
    M static/maps/mvc/workflow/workflow-node.js.map
    M static/maps/mvc/workflow/workflow-view-node.js.map
    M static/maps/mvc/workflow/workflow-view.js.map
    M static/maps/polyfills.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/bundled/libs.bundled.js
    M static/scripts/bundled/libs.bundled.js.map
    M static/scripts/mvc/base-mvc.js
    M static/scripts/mvc/citation/citation-model.js
    M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
    M static/scripts/mvc/ui/ui-select-default.js
    M static/scripts/mvc/workflow/workflow-manager.js
    M static/scripts/mvc/workflow/workflow-node.js
    M static/scripts/mvc/workflow/workflow-view-node.js
    M static/scripts/mvc/workflow/workflow-view.js
    M static/scripts/polyfills.js
    M static/style/blue/base.css
    R templates/webapps/galaxy/history/options.mako
    M templates/webapps/galaxy/workflow/editor_generic_form.mako
    M test/api/test_tools.py
    M test/api/test_workflows.py
    M test/api/workflows_format_2/converter.py
    M test/base/interactor.py
    M test/docker/base/Dockerfile
    M test/docker/base/run_test_wrapper.sh
    M test/qunit/tests/workflow_editor_tests.js
    M test/tool_shed/functional/test_1460_data_managers.py
    M test/unit/managers/test_UserManager.py
    M test/unit/tools/test_tool_deps.py
    M test/unit/workflows/test_modules.py
    M tox.ini

  Log Message:
  -----------
  Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004


  Commit: b8d7cf035df49f2fda9291b91eadf59fd48bfdd0
      https://github.com/galaxyproject/galaxy/commit/b8d7cf035df49f2fda9291b91eadf...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-14 (Mon, 14 Dec 2015)

  Changed paths:
    M config/galaxy.ini.sample
    M templates/webapps/galaxy/workflow/run.mako

  Log Message:
  -----------
  Add config setting, disable by default


  Commit: 42edfca679f204aa7e69a6c3df6dc14c8118e22c
      https://github.com/galaxyproject/galaxy/commit/42edfca679f204aa7e69a6c3df6dc...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-14 (Mon, 14 Dec 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/workflow/workflow-view.js
    M lib/galaxy/tools/__init__.py
    M static/maps/mvc/workflow/workflow-view.js.map
    M static/scripts/mvc/workflow/workflow-view.js

  Log Message:
  -----------
  Repack, refix section validation


  Commit: 10fff14ce5ba6952f21da10c81a31ceda397a666
      https://github.com/galaxyproject/galaxy/commit/10fff14ce5ba6952f21da10c81a31...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-14 (Mon, 14 Dec 2015)

  Changed paths:
    M templates/webapps/galaxy/workflow/run.mako

  Log Message:
  -----------
  Fix missing wf parameter issue in classic form


  Commit: 57bc4660cf4e21ebe8b73035095e021e4f298680
      https://github.com/galaxyproject/galaxy/commit/57bc4660cf4e21ebe8b73035095e0...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-14 (Mon, 14 Dec 2015)

  Changed paths:
    M lib/galaxy/tools/parameters/basic.py

  Log Message:
  -----------
  Fix workflow parameter validation


  Commit: 3108ba5c01ded7b0209685f57ab231c2cfe92938
      https://github.com/galaxyproject/galaxy/commit/3108ba5c01ded7b0209685f57ab23...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-14 (Mon, 14 Dec 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/ui/ui-misc.js
    M static/maps/mvc/ui/ui-misc.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/bundled/libs.bundled.js.map
    M static/scripts/mvc/ui/ui-misc.js

  Log Message:
  -----------
  Ensure that text fields only display text


  Commit: a440813e37941d050ac503a0898dcf00c5f1b4fe
      https://github.com/galaxyproject/galaxy/commit/a440813e37941d050ac503a0898dc...
  Author: guerler <aysam.guerler@gmail.com>
  Date:   2015-12-14 (Mon, 14 Dec 2015)

  Changed paths:
    M lib/galaxy/tools/parameters/basic.py

  Log Message:
  -----------
  Add workflow_mode flag to validation


  Commit: e838b03300964615bc2144ceeb9ba785cf5f7a7d
      https://github.com/galaxyproject/galaxy/commit/e838b03300964615bc2144ceeb9ba...
  Author: John Chilton <jmchilton@gmail.com>
  Date:   2015-12-14 (Mon, 14 Dec 2015)

  Changed paths:
    M client/galaxy/scripts/apps/analysis.js
    M client/galaxy/scripts/mvc/dataset/dataset-li-edit.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-repeat.js
    M client/galaxy/scripts/mvc/form/form-section.js
    M client/galaxy/scripts/mvc/form/form-select-content.js
    M client/galaxy/scripts/mvc/form/form-view.js
    A client/galaxy/scripts/mvc/tool/tool-form-base.js
    A client/galaxy/scripts/mvc/tool/tool-form-composite.js
    A client/galaxy/scripts/mvc/tool/tool-form-workflow.js
    A client/galaxy/scripts/mvc/tool/tool-form.js
    A client/galaxy/scripts/mvc/tool/tool-template.js
    R client/galaxy/scripts/mvc/tool/tools-form-base.js
    R client/galaxy/scripts/mvc/tool/tools-form-workflow.js
    R client/galaxy/scripts/mvc/tool/tools-form.js
    R client/galaxy/scripts/mvc/tool/tools-jobs.js
    R client/galaxy/scripts/mvc/tool/tools-template.js
    M client/galaxy/scripts/mvc/tool/tools.js
    M client/galaxy/scripts/mvc/ui/ui-drilldown.js
    M client/galaxy/scripts/mvc/ui/ui-misc.js
    M client/galaxy/scripts/mvc/ui/ui-portlet.js
    M client/galaxy/scripts/mvc/ui/ui-slider.js
    M client/galaxy/scripts/mvc/workflow/workflow-view.js
    M client/galaxy/scripts/utils/utils.js
    M client/galaxy/style/less/ui.less
    M config/galaxy.ini.sample
    M config/plugins/visualizations/charts/static/build-app.js
    M config/plugins/visualizations/charts/static/library/ui-table-form.js
    M config/plugins/visualizations/charts/static/views/editor.js
    M lib/galaxy/tools/__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/webapps/galaxy/api/workflows.py
    A static/maps/galaxy-app-base.js.map
    M static/maps/mvc/dataset/dataset-li-edit.js.map
    M static/maps/mvc/form/form-data.js.map
    M static/maps/mvc/form/form-input.js.map
    M static/maps/mvc/form/form-parameters.js.map
    M static/maps/mvc/form/form-repeat.js.map
    M static/maps/mvc/form/form-section.js.map
    M static/maps/mvc/form/form-select-content.js.map
    M static/maps/mvc/form/form-view.js.map
    A static/maps/mvc/tool/tool-form-base.js.map
    A static/maps/mvc/tool/tool-form-composite.js.map
    A static/maps/mvc/tool/tool-form-workflow.js.map
    A static/maps/mvc/tool/tool-form.js.map
    A static/maps/mvc/tool/tool-template.js.map
    R static/maps/mvc/tool/tools-form-base.js.map
    R static/maps/mvc/tool/tools-form-workflow.js.map
    R static/maps/mvc/tool/tools-form.js.map
    R static/maps/mvc/tool/tools-jobs.js.map
    R static/maps/mvc/tool/tools-template.js.map
    M static/maps/mvc/tool/tools.js.map
    R static/maps/mvc/tools.js.map
    R static/maps/mvc/tools/tools-form-base.js.map
    M static/maps/mvc/ui/ui-drilldown.js.map
    M static/maps/mvc/ui/ui-misc.js.map
    M static/maps/mvc/ui/ui-portlet.js.map
    M static/maps/mvc/ui/ui-slider.js.map
    M static/maps/mvc/workflow/workflow-view.js.map
    M static/maps/utils/utils.js.map
    M static/scripts/bundled/analysis.bundled.js
    M static/scripts/bundled/analysis.bundled.js.map
    M static/scripts/bundled/libs.bundled.js
    M static/scripts/bundled/libs.bundled.js.map
    M static/scripts/bundled/login.bundled.js
    M static/scripts/bundled/login.bundled.js.map
    M static/scripts/mvc/dataset/dataset-li-edit.js
    M static/scripts/mvc/form/form-data.js
    M static/scripts/mvc/form/form-input.js
    M static/scripts/mvc/form/form-parameters.js
    M static/scripts/mvc/form/form-repeat.js
    M static/scripts/mvc/form/form-section.js
    M static/scripts/mvc/form/form-select-content.js
    M static/scripts/mvc/form/form-view.js
    A static/scripts/mvc/tool/tool-form-base.js
    A static/scripts/mvc/tool/tool-form-composite.js
    A static/scripts/mvc/tool/tool-form-workflow.js
    A static/scripts/mvc/tool/tool-form.js
    A static/scripts/mvc/tool/tool-template.js
    R static/scripts/mvc/tool/tools-form-base.js
    R static/scripts/mvc/tool/tools-form-workflow.js
    R static/scripts/mvc/tool/tools-form.js
    R static/scripts/mvc/tool/tools-jobs.js
    R static/scripts/mvc/tool/tools-template.js
    M static/scripts/mvc/tool/tools.js
    R static/scripts/mvc/tools.js
    R static/scripts/mvc/tools/tools-form-base.js
    M static/scripts/mvc/ui/ui-drilldown.js
    M static/scripts/mvc/ui/ui-misc.js
    M static/scripts/mvc/ui/ui-portlet.js
    M static/scripts/mvc/ui/ui-slider.js
    M static/scripts/mvc/workflow/workflow-view.js
    M static/scripts/utils/utils.js
    M static/style/blue/base.css
    M templates/webapps/galaxy/workflow/editor_tool_form.mako
    M templates/webapps/galaxy/workflow/run.mako

  Log Message:
  -----------
  Merge pull request #1249 from guerler/run_workflow_form_004

Run workflow form


Compare: https://github.com/galaxyproject/galaxy/compare/0fce226b96f9...e838b0330096

[galaxy-commits] [galaxyproject/galaxy] 458766: Add run workflow tool form

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