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[hg] galaxy 3724: Change the way size of output file determined ...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/007f175c8b88 changeset: 3724:007f175c8b88 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Apr 30 15:27:41 2010 -0400 description: Change the way size of output file determined in Bowtie and SAM-to_BAM to deal with memory limitation. diffstat: tools/samtools/sam_to_bam.py | 2 +- tools/sr_mapping/bowtie_wrapper.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diffs (26 lines): diff -r 85e05920bada -r 007f175c8b88 tools/samtools/sam_to_bam.py --- a/tools/samtools/sam_to_bam.py Fri Apr 30 15:20:04 2010 -0400 +++ b/tools/samtools/sam_to_bam.py Fri Apr 30 15:27:41 2010 -0400 @@ -94,7 +94,7 @@ tmp_stderr.close() if returncode != 0: raise Exception, stderr - if len( open( fai_index_file_path ).read().strip() ) == 0: + if os.path.getsize( fai_index_file_path ) == 0: raise Exception, 'Index file empty, there may be an error with your reference file or settings.' except Exception, e: #clean up temp files diff -r 85e05920bada -r 007f175c8b88 tools/sr_mapping/bowtie_wrapper.py --- a/tools/sr_mapping/bowtie_wrapper.py Fri Apr 30 15:20:04 2010 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.py Fri Apr 30 15:27:41 2010 -0400 @@ -387,8 +387,8 @@ if returncode != 0: raise Exception, stderr # check that there are results in the output file - if len( open( options.output, 'rb' ).read().strip() ) == 0: - raise Exception, 'The output file is empty, there may be an error with your input file or settings.' + if os.path.getsize( options.output ) == 0: + raise Exception, 'The output file is empty, there may be an error with your input file or settings.' + '\nextra: ' + str(extra) except Exception, e: stop_err( 'Error aligning sequence. ' + str( e ) ) finally:

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[hg] galaxy 3723: Add a link to the user's uploaded tools from t...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/85e05920bada changeset: 3723:85e05920bada user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Apr 30 15:20:04 2010 -0400 description: Add a link to the user's uploaded tools from the Manage users grid, and fix some more bugs in the community app. diffstat: lib/galaxy/webapps/community/controllers/admin.py | 60 ++++++---------------- templates/webapps/community/index.mako | 4 +- templates/webapps/community/tool/edit_tool.mako | 1 - templates/webapps/community/tool/view_tool.mako | 1 - 4 files changed, 20 insertions(+), 46 deletions(-) diffs (148 lines): diff -r db4f8befcd89 -r 85e05920bada lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 30 14:08:23 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 30 15:20:04 2010 -0400 @@ -18,13 +18,6 @@ if user.username: return user.username return 'not set' - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): - if user.purged: - return "purged" - elif user.deleted: - return "deleted" - return "" class GroupsColumn( grids.GridColumn ): def get_value( self, trans, grid, user ): if user.groups: @@ -45,6 +38,16 @@ if user.galaxy_sessions: return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + if user.purged: + return "purged" + elif user.deleted: + return "deleted" + return "" + class ToolsColumn( grids.TextColumn ): + def get_value( self, trans, grid, user ): + return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( user.id ), str( len( user.tools ) ) ) # Grid definition webapp = "community" @@ -69,6 +72,10 @@ ExternalColumn( "External", attach_popup=False ), LastLoginColumn( "Last Login", format=time_ago ), StatusColumn( "Status", attach_popup=False ), + ToolsColumn( "Uploaded Tools", + model_class=model.User, + attach_popup=False, + filterable="advanced" ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] @@ -488,11 +495,7 @@ grids.GridOperation( "Edit information", condition=( lambda item: not item.deleted ), allow_multiple=False, - url_args=dict( controller="common", action="edit_tool", cntrller="admin", webapp="community" ) ), - grids.GridOperation( "Manage categories", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( controller="common", action="manage_categories", cntrller="admin", webapp="community" ) ) + url_args=dict( controller="common", action="edit_tool", cntrller="admin", webapp="community" ) ) ] standard_filters = [ grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), @@ -553,7 +556,6 @@ @web.expose @web.require_admin def browse_tools_by_user( self, trans, **kwd ): - # TODO: move this to the common controller as it is in the tool controller as well... if 'operation' in kwd: operation = kwd['operation'].lower() if operation == "browse": @@ -580,35 +582,8 @@ return trans.response.send_redirect( web.url_for( controller='tool', action='download_tool', **kwd ) ) - @web.expose - @web.require_admin - def browse_tools_by_user( self, trans, **kwd ): - # TODO: move this to the common controller as it is in the tool controller as well... - if 'operation' in kwd: - operation = kwd['operation'].lower() - if operation == "browse": - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_tools_by_user', - **kwd ) ) - elif operation == "browse category": - return trans.response.send_redirect( web.url_for( controller='common', - action='browse_category', - cntrller='admin', - **kwd ) ) - elif operation == "view tool": - return trans.response.send_redirect( web.url_for( controller='common', - action='view_tool', - cntrller='admin', - **kwd ) ) - elif operation == "edit tool": - return trans.response.send_redirect( web.url_for( controller='common', - action='edit_tool', - cntrller='admin', - **kwd ) ) - elif operation == "download tool": - return trans.response.send_redirect( web.url_for( controller='tool', - action='download_tool', - **kwd ) ) + # Render the list view + return self.tool_list_grid( trans, **kwd ) @web.expose @web.require_admin def manage_categories( self, trans, **kwd ): @@ -860,7 +835,6 @@ ## ---- Utility methods ------------------------------------------------------- def get_tools_by_state( trans, state ): - # TODO: this can be written so that it is much cleaner and faster tool_id = [] if state == trans.model.Tool.states.NEW: for tool in get_tools( trans ): diff -r db4f8befcd89 -r 85e05920bada templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako Fri Apr 30 14:08:23 2010 -0400 +++ b/templates/webapps/community/index.mako Fri Apr 30 15:20:04 2010 -0400 @@ -82,7 +82,9 @@ <div class="toolSectionBg"> <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_categories' )}">Browse by category</a></div> <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_tools' )}">Browse all tools</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_tools_by_user', operation='browse', id=trans.security.encode_id( trans.user.id ) )}">Browse your tools</a></div> + %if trans.user: + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_tools_by_user', operation='browse', id=trans.security.encode_id( trans.user.id ) )}">Browse your tools</a></div> + %endif </div> </div> <div class="toolSectionBody"> diff -r db4f8befcd89 -r 85e05920bada templates/webapps/community/tool/edit_tool.mako --- a/templates/webapps/community/tool/edit_tool.mako Fri Apr 30 14:08:23 2010 -0400 +++ b/templates/webapps/community/tool/edit_tool.mako Fri Apr 30 15:20:04 2010 -0400 @@ -58,7 +58,6 @@ <a id="tool-${tool.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="tool-${tool.id}-popup"> <a class="action-button" href="${h.url_for( controller='common', action='view_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">View information</a> - <a class="action-button" href="${h.url_for( controller='common', action='manage_categories', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Manage categories</a> <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> </div> diff -r db4f8befcd89 -r 85e05920bada templates/webapps/community/tool/view_tool.mako --- a/templates/webapps/community/tool/view_tool.mako Fri Apr 30 14:08:23 2010 -0400 +++ b/templates/webapps/community/tool/view_tool.mako Fri Apr 30 15:20:04 2010 -0400 @@ -67,7 +67,6 @@ <div popupmenu="tool-${tool.id}-popup"> %if cntrller=='admin' or can_edit: <a class="action-button" href="${h.url_for( controller='common', action='edit_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Edit information</a> - <a class="action-button" href="${h.url_for( controller='common', action='manage_categories', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Manage categories</a> <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> %endif <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a>

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[hg] galaxy 3722: Many fixes and additional features added to th...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/db4f8befcd89 changeset: 3722:db4f8befcd89 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Apr 30 14:08:23 2010 -0400 description: Many fixes and additional features added to the community. diffstat: lib/galaxy/webapps/community/controllers/admin.py | 374 +++++++++++-- lib/galaxy/webapps/community/controllers/common.py | 81 ++- lib/galaxy/webapps/community/controllers/tool.py | 293 ++++++++-- lib/galaxy/webapps/community/model/__init__.py | 7 +- lib/galaxy/webapps/community/model/mapping.py | 5 +- templates/webapps/community/admin/index.mako | 43 +- templates/webapps/community/category/edit_category.mako | 44 + templates/webapps/community/category/rename_category.mako | 44 - templates/webapps/community/index.mako | 62 ++- templates/webapps/community/tool/browse_tool.mako | 37 - templates/webapps/community/tool/edit_tool.mako | 2 +- templates/webapps/community/tool/view_tool.mako | 8 + 12 files changed, 733 insertions(+), 267 deletions(-) diffs (1467 lines): diff -r c642fbb301fc -r db4f8befcd89 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 30 13:09:29 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 30 14:08:23 2010 -0400 @@ -2,7 +2,7 @@ from galaxy.webapps.community import model from galaxy.model.orm import * from galaxy.web.framework.helpers import time_ago, iff, grids -from common import get_categories, get_category +from common import get_categories, get_category, get_tools, get_event, get_tool import logging log = logging.getLogger( __name__ ) @@ -200,7 +200,7 @@ return None def build_initial_query( self, session ): return session.query( self.model_class ) - def apply_default_filter( self, trans, query, **kwargs ): + def apply_default_filter( self, trans, query, **kwd ): return query.filter( model.Role.type != model.Role.types.PRIVATE ) class GroupListGrid( grids.Grid ): @@ -280,34 +280,31 @@ def build_initial_query( self, session ): return session.query( self.model_class ) -class CategoryListGrid( grids.Grid ): +class ManageCategoryListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.name class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.description - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, category ): - if category.deleted: - return "deleted" - return "" # Grid definition webapp = "community" - title = "Categories" + title = "Manage Categories" model_class = model.Category template='/webapps/community/category/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", key="name", - link=( lambda item: dict( operation="Edit category", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="Edit", id=item.id, webapp="community" ) ), model_class=model.Category, - attach_popup=True, + attach_popup=False, filterable="advanced" ), - DescriptionColumn( "Description", attach_popup=False ), - StatusColumn( "Status", attach_popup=False ), + DescriptionColumn( "Description", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] @@ -318,13 +315,9 @@ filterable="standard" ) ) global_actions = [ grids.GridAction( "Add new category", - dict( controller='admin', action='categories', operation='create', webapp="community" ) ) + dict( controller='admin', action='manage_categories', operation='create', webapp="community" ) ) ] - operations = [ grids.GridOperation( "Rename", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( webapp="community", action="rename_category" ) ), - grids.GridOperation( "Delete", + operations = [ grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True, url_args=dict( webapp="community", action="mark_category_deleted" ) ), @@ -349,16 +342,77 @@ def build_initial_query( self, session ): return session.query( self.model_class ) +class ToolsByCategoryListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + return category.name + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + return category.description + class ToolsColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + if category.tools: + return len( category.tools ) + return 0 + + # Grid definition + webapp = "community" + title = "Tools by Category" + model_class = model.Category + template='/webapps/community/category/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="Browse Category", id=item.id, webapp="community" ) ), + model_class=model.Category, + attach_popup=True, + filterable="advanced" ), + DescriptionColumn( "Description", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), + ToolsColumn( "Tools", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1], columns[2] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def get_current_item( self, trans ): + return None + def build_initial_query( self, session ): + return session.query( self.model_class ) + class ToolListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): return tool.name + class VersionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.version + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.description class CategoryColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): if tool.categories: rval = '' for tca in tool.categories: - rval = '%s%s<br/>' % ( rval, tca.category.name ) + rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) return rval return 'not set' class StateColumn( grids.GridColumn ): @@ -389,7 +443,7 @@ return accepted_filters class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - return tool.user.email + return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) # Grid definition title = "Tools" model_class = model.Tool @@ -402,27 +456,34 @@ link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='admin', webapp="community" ) ), attach_popup=True, filterable="advanced" ), + VersionColumn( "Version", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + DescriptionColumn( "Description", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), CategoryColumn( "Category", - key="category", model_class=model.Category, attach_popup=False, filterable="advanced" ), - StateColumn( "State", - key="state", + StateColumn( "Status", model_class=model.Event, - attach_popup=False, - filterable="advanced" ), + attach_popup=False ), + UserColumn( "Uploaded By", + key="username", + model_class=model.User, + attach_popup=False, + filterable="advanced" ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", model_class=model.Tool, key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, filterable="standard" ) ) - global_actions = [ - grids.GridAction( "Upload tool", dict( controller='upload', action='upload', type='tool' ) ) - ] operations = [ grids.GridOperation( "Edit information", condition=( lambda item: not item.deleted ), @@ -443,57 +504,156 @@ use_paging = True def build_initial_query( self, session ): return session.query( self.model_class ) - def apply_default_filter( self, trans, query, **kwargs ): + def apply_default_filter( self, trans, query, **kwd ): + tool_id = kwd.get( 'tool_id', False ) + if tool_id: + if str( tool_id ).lower() in [ '', 'none' ]: + # Return an empty query since the current user cannot view any + # tools (possibly due to state not being approved, etc). + return query.filter( model.Tool.id == None ) + tool_id = util.listify( tool_id ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) return query.filter( self.model_class.deleted==False ) -class AdminCommunity( BaseController, Admin ): +class AdminController( BaseController, Admin ): user_list_grid = UserListGrid() role_list_grid = RoleListGrid() group_list_grid = GroupListGrid() - category_list_grid = CategoryListGrid() + manage_category_list_grid = ManageCategoryListGrid() + tools_by_category_list_grid = ToolsByCategoryListGrid() tool_list_grid = ToolListGrid() @web.expose @web.require_admin - def browse_tools( self, trans, **kwargs ): - if 'operation' in kwargs: - operation = kwargs['operation'].lower() + def browse_tools( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "edit tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_tool', + cntrller='admin', + **kwd ) ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='view_tool', + cntrller='admin', + **kwd ) ) + # Render the list view + return self.tool_list_grid( trans, **kwd ) + @web.expose + @web.require_admin + def browse_tools_by_category( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "browse category": + return self.browse_category( trans, id=kwd['id'] ) + # Render the list view + return self.tools_by_category_list_grid( trans, **kwd ) + @web.expose + @web.require_admin + def browse_tools_by_user( self, trans, **kwd ): + # TODO: move this to the common controller as it is in the tool controller as well... + if 'operation' in kwd: + operation = kwd['operation'].lower() if operation == "browse": - return trans.response.send_redirect( web.url_for( controller='tool', - action='browse_tools', + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_tools_by_user', cntrller='admin', - **kwargs ) ) + **kwd ) ) + elif operation == "browse category": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='admin', + **kwd ) ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='view_tool', + cntrller='admin', + **kwd ) ) elif operation == "edit tool": return trans.response.send_redirect( web.url_for( controller='common', action='edit_tool', cntrller='admin', - **kwargs ) ) + **kwd ) ) + elif operation == "download tool": + return trans.response.send_redirect( web.url_for( controller='tool', + action='download_tool', + **kwd ) ) + @web.expose + @web.require_admin + def browse_tools_by_user( self, trans, **kwd ): + # TODO: move this to the common controller as it is in the tool controller as well... + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "browse": + return trans.response.send_redirect( web.url_for( controller='admin', + action='browse_tools_by_user', + **kwd ) ) + elif operation == "browse category": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='admin', + **kwd ) ) elif operation == "view tool": return trans.response.send_redirect( web.url_for( controller='common', action='view_tool', cntrller='admin', - **kwargs ) ) - # Render the list view - return self.tool_list_grid( trans, **kwargs ) + **kwd ) ) + elif operation == "edit tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_tool', + cntrller='admin', + **kwd ) ) + elif operation == "download tool": + return trans.response.send_redirect( web.url_for( controller='tool', + action='download_tool', + **kwd ) ) @web.expose @web.require_admin - def categories( self, trans, **kwargs ): - if 'operation' in kwargs: - operation = kwargs['operation'].lower() + def manage_categories( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() if operation == "create": - return self.create_category( trans, **kwargs ) + return self.create_category( trans, **kwd ) if operation == "delete": - return self.mark_category_deleted( trans, **kwargs ) + return self.mark_category_deleted( trans, **kwd ) if operation == "undelete": - return self.undelete_category( trans, **kwargs ) + return self.undelete_category( trans, **kwd ) if operation == "purge": - return self.purge_category( trans, **kwargs ) - if operation == "rename": - return self.rename_category( trans, **kwargs ) + return self.purge_category( trans, **kwd ) + if operation == "edit": + return self.edit_category( trans, **kwd ) # Render the list view - return self.category_list_grid( trans, **kwargs ) - + return self.manage_category_list_grid( trans, **kwd ) + @web.expose + @web.require_admin + def browse_tools_by_state( self, trans, state=None, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + if state is None: + id = params.get( 'id', None ) + if not id: + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + message='Select a status', + status='error' ) ) + event = get_event( trans, id ) + state = event.state + tool_id = get_tools_by_state( trans, state ) + if not tool_id: + tool_id = 'None' + return trans.response.send_redirect( web.url_for( controller='admin', + action='browse_tools', + tool_id=tool_id ) ) + @web.expose + @web.require_admin + def browse_category( self, trans, **kwd ): + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='admin', + **kwd ) ) @web.expose @web.require_admin def create_category( self, trans, **kwd ): @@ -515,7 +675,7 @@ message = "Category '%s' has been created" % category.name trans.sa_session.flush() trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) @@ -530,42 +690,69 @@ status=status ) @web.expose @web.require_admin - def rename_category( self, trans, **kwd ): + def set_tool_state( self, trans, state, **kwd ): params = util.Params( kwd ) webapp = params.get( 'webapp', 'galaxy' ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) id = params.get( 'id', None ) if not id: - message = "No category ids received for renaming" + message = "No tool id received for setting status" + status = 'error' + else: + tool = get_tool( trans, id ) + event = trans.model.Event( state ) + # Flush so we an get an id + trans.sa_session.add( event ) + trans.sa_session.flush() + tea = trans.model.ToolEventAssociation( tool, event ) + trans.sa_session.add( tea ) + trans.sa_session.flush() + message = "State of tool '%s' is now %s" % ( tool.name, state ) + trans.response.send_redirect( web.url_for( controller='admin', + action='browse_tools', + webapp=webapp, + message=message, + status=status ) ) + @web.expose + @web.require_admin + def edit_category( self, trans, **kwd ): + params = util.Params( kwd ) + webapp = params.get( 'webapp', 'galaxy' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = params.get( 'id', None ) + if not id: + message = "No category ids received for editing" trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=message, status='error' ) ) category = get_category( trans, id ) - if params.get( 'rename_category_button', False ): + if params.get( 'edit_category_button', False ): old_name = category.name new_name = util.restore_text( params.name ) new_description = util.restore_text( params.description ) - if not new_name: - message = 'Enter a valid name' - status = 'error' - elif trans.sa_session.query( trans.app.model.Category ).filter( trans.app.model.Category.table.c.name==new_name ).first(): - message = 'A category with that name already exists' - status = 'error' + if old_name != new_name: + if not new_name: + message = 'Enter a valid name' + status = 'error' + elif trans.sa_session.query( trans.app.model.Category ).filter( trans.app.model.Category.table.c.name==new_name ).first(): + message = 'A category with that name already exists' + status = 'error' else: category.name = new_name category.description = new_description trans.sa_session.add( category ) trans.sa_session.flush() - message = "Category '%s' has been renamed to '%s'" % ( old_name, new_name ) + message = "The information has been saved for category '%s'" % ( new_name ) return trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) - return trans.fill_template( '/webapps/community/category/rename_category.mako', + return trans.fill_template( '/webapps/community/category/edit_category.mako', category=category, webapp=webapp, message=message, @@ -579,7 +766,7 @@ if not id: message = "No category ids received for deleting" trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=message, status='error' ) ) @@ -592,7 +779,7 @@ trans.sa_session.flush() message += " %s " % category.name trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) @@ -605,7 +792,7 @@ if not id: message = "No category ids received for undeleting" trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=message, status='error' ) ) @@ -617,7 +804,7 @@ if not category.deleted: message = "Category '%s' has not been deleted, so it cannot be undeleted." % category.name trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='error' ) ) @@ -628,7 +815,7 @@ undeleted_categories += " %s" % category.name message = "Undeleted %d categories: %s" % ( count, undeleted_categories ) trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) @@ -644,7 +831,7 @@ if not id: message = "No category ids received for purging" trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='error' ) ) @@ -655,7 +842,7 @@ if not category.deleted: message = "Category '%s' has not been deleted, so it cannot be purged." % category.name trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='error' ) ) @@ -665,7 +852,42 @@ trans.sa_session.flush() message += " %s " % category.name trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) + +## ---- Utility methods ------------------------------------------------------- + +def get_tools_by_state( trans, state ): + # TODO: this can be written so that it is much cleaner and faster + tool_id = [] + if state == trans.model.Tool.states.NEW: + for tool in get_tools( trans ): + if tool.is_new(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.ERROR: + for tool in get_tools( trans ): + if tool.is_error(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.DELETED: + for tool in get_tools( trans ): + if tool.is_deleted(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.WAITING: + for tool in get_tools( trans ): + if tool.is_waiting(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.APPROVED: + for tool in get_tools( trans ): + if tool.is_approved(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.REJECTED: + for tool in get_tools( trans ): + if tool.is_rejected(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.ARCHIVED: + for tool in get_tools( trans ): + if tool.is_archived(): + tool_id.append( tool.id ) + return tool_id diff -r c642fbb301fc -r db4f8befcd89 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py Fri Apr 30 13:09:29 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Fri Apr 30 14:08:23 2010 -0400 @@ -8,7 +8,7 @@ import logging log = logging.getLogger( __name__ ) -class CommunityCommon( BaseController ): +class CommonController( BaseController ): @web.expose def edit_tool( self, trans, cntrller, **kwd ): params = util.Params( kwd ) @@ -108,6 +108,54 @@ action='browse_tools', message='Not yet implemented, sorry...', status='error' ) ) + @web.expose + def browse_category( self, trans, cntrller, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = params.get( 'id', None ) + if not id: + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_categories', + message='Select a category', + status='error' ) ) + category = get_category( trans, id ) + # If request came from the tool controller, then we need to filter by the state of the + # tool in addition to the category. + if cntrller == 'tool': + tool_id = get_approved_tools( trans, category=category ) + else: + # If request came from the admin controller, we don't filter on tool state. + tool_id = [ tca.tool.id for tca in category.tools ] + if not tool_id: + tool_id = 'None' + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + tool_id=tool_id ) ) + @web.expose + def browse_tools_by_user( self, trans, cntrller, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = params.get( 'id', None ) + if not id: + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + message='Select a user', + status='error' ) ) + user = get_user( trans, id ) + # If request came from the tool controller, then we need to filter by the state of the + # tool if the user is not viewing his own tools + if cntrller == 'tool': + tool_id = get_approved_tools( trans, user=user ) + else: + # If request came from the admin controller, we don't filter on tool state. + tool_id = [ tool.id for tool in user.tools ] + if not tool_id: + tool_id = 'None' + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools_by_user', + tool_id=tool_id ) ) ## ---- Utility methods ------------------------------------------------------- @@ -142,4 +190,33 @@ obj.categories.append( trans.model.ToolCategoryAssociation( obj, category ) ) def get_tool( trans, id ): return trans.sa_session.query( trans.model.Tool ).get( trans.app.security.decode_id( id ) ) - +def get_tools( trans ): + return trans.sa_session.query( trans.model.Tool ).order_by( trans.model.Tool.name ) +def get_approved_tools( trans, category=None, user=None ): + tool_id = [] + if category: + # Return only the approved tools in the category + for tca in category.tools: + tool = tca.tool + if tool.is_approved(): + tool_id.append( tool.id ) + elif user: + if trans.user == user: + # If the current user is browsing his own tools, then don't filter on state + tool_id = [ tool.id for tool in user.tools ] + else: + # The current user is viewing all tools uploaded by another user, so show only + # approved tools + for tool in user.active_tools: + if tool.is_approved(): + tool_id.append( tool.id ) + else: + # Return all approved tools + for tool in get_tools( trans ): + if tool.is_approved(): + tool_id.append( tool.id ) + return tool_id +def get_event( trans, id ): + return trans.sa_session.query( trans.model.Event ).get( trans.security.decode_id( id ) ) +def get_user( trans, id ): + return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) diff -r c642fbb301fc -r db4f8befcd89 lib/galaxy/webapps/community/controllers/tool.py --- a/lib/galaxy/webapps/community/controllers/tool.py Fri Apr 30 13:09:29 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/tool.py Fri Apr 30 14:08:23 2010 -0400 @@ -15,38 +15,111 @@ class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): return tool.name + class VersionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.version + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.description class CategoryColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): if tool.categories: rval = '' for tca in tool.categories: - rval += '%s<br/>\n' % tca.category.name + rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) return rval return 'not set' - def filter( self, trans, user, query, column_filter ): - # Category.name conflicts with Tool.name, so we have to make our own filter - def get_single_filter( filter ): - return func.lower( model.Category.name ).like( "%" + filter.lower() + "%" ) - if column_filter == 'All': - pass - elif isinstance( column_filter, list ): - clause_list = [] - for filter in column_filter: - clause_list.append( get_single_filter( filter ) ) - query = query.filter( or_( *clause_list ) ) - else: - query = query.filter( get_single_filter( column_filter ) ) - return query - def get_link( self, trans, grid, tool, filter_params ): + class UserColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) + # Grid definition + title = "Tools" + model_class = model.Tool + template='/webapps/community/tool/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="name", + model_class=model.Tool, + link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='tool', webapp="community" ) ), + attach_popup=True, + filterable="advanced" ), + VersionColumn( "Version", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + DescriptionColumn( "Description", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + CategoryColumn( "Categories", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), + UserColumn( "Uploaded By", + key="username", + model_class=model.User, + attach_popup=False, + filterable="advanced" ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [ + grids.GridOperation( "Download tool", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( controller="tool", action="download_tool", cntrller="tool", webapp="community" ) ) + ] + standard_filters = [ + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + default_filter = dict( name="All", deleted="False", username="All" ) + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def build_initial_query( self, session ): + return session.query( self.model_class ) + def apply_default_filter( self, trans, query, **kwd ): + def filter_query( query, tool_id ): + if str( tool_id ).lower() in [ '', 'none' ]: + # Return an empty query since the current user cannot view any + # tools (possibly due to state not being approved, etc). + return query.filter( model.Tool.id == None ) + tool_id = util.listify( tool_id ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) + return query.filter( self.model_class.deleted==False ) + tool_id = kwd.get( 'tool_id', False ) + if not tool_id: + # Display only approved tools + tool_id = get_approved_tools( trans ) + if not tool_id: + tool_id = 'None' + return filter_query( query, tool_id ) + +class ToolsByUserListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.name + class VersionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.version + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.description + class CategoryColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): if tool.categories: - filter_params['f-category'] = [] + rval = '' for tca in tool.categories: - filter_params['f-category'].append( tca.category.name ) - if len( filter_params['f-category'] ) == 1: - filter_params['f-category'] = filter_params['f-category'][0] - filter_params['advanced-search'] = 'True' - return filter_params - return None + rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) + return rval + return 'not set' class StateColumn( grids.GridColumn ): def get_value( self, trans, grid, tool ): state = tool.state() @@ -75,13 +148,9 @@ return accepted_filters class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - return tool.user.username - def get_link( self, trans, grid, tool, filter_params ): - filter_params['f-username'] = tool.user.username - filter_params['advanced-search'] = 'True' - return filter_params + return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) # Grid definition - title = "Tools" + title = "Tools By User" model_class = model.Tool template='/webapps/community/tool/grid.mako' default_sort_key = "name" @@ -92,21 +161,26 @@ link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='tool', webapp="community" ) ), attach_popup=True, filterable="advanced" ), - CategoryColumn( "Categories", - key="category", + VersionColumn( "Version", model_class=model.Tool, attach_popup=False, filterable="advanced" ), + DescriptionColumn( "Description", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + CategoryColumn( "Categories", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), + StateColumn( "Status", + model_class=model.Event, + attach_popup=False ), UserColumn( "Uploaded By", key="username", model_class=model.User, attach_popup=False, filterable="advanced" ), - StateColumn( "State", - key="state", - model_class=model.Event, - attach_popup=False, - filterable="advanced" ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] @@ -130,18 +204,44 @@ preserve_state = False use_paging = True def build_initial_query( self, session ): - return session.query( self.model_class ).outerjoin( model.ToolCategoryAssociation ).outerjoin( model.Category ) - def apply_default_filter( self, trans, query, **kwargs ): - return query.filter( self.model_class.deleted==False ) + return session.query( self.model_class ) + def apply_default_filter( self, trans, query, **kwd ): + def filter_query( query, tool_id ): + if str( tool_id ).lower() in [ '', 'none' ]: + # Return an empty query since the current user cannot view any + # tools (possibly due to state not being approved, etc). + return query.filter( model.Tool.id == None ) + tool_id = util.listify( tool_id ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) + return query.filter( self.model_class.deleted==False ) + tool_id = kwd.get( 'tool_id', False ) + if not tool_id: + # Display only approved tools + tool_id = get_approved_tools( trans ) + if not tool_id: + tool_id = 'None' + return filter_query( query, tool_id ) -class ToolCategoryListGrid( grids.Grid ): +class CategoryListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.name class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.description + class ToolsColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + if category.tools: + viewable_tools = 0 + for tca in category.tools: + tool = tca.tool + if tool.is_approved(): + viewable_tools += 1 + return viewable_tools + return 0 + # Grid definition + webapp = "community" title = "Tool Categories" model_class = model.Category template='/webapps/community/category/grid.mako' @@ -157,7 +257,13 @@ key="description", model_class=model.Category, attach_popup=False, - filterable="advanced" ) + filterable="advanced" ), + ToolsColumn( "Tools", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], @@ -165,21 +271,23 @@ visible=False, filterable="standard" ) ) standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) ] - default_filter = dict( name="All", deleted="False" ) num_rows_per_page = 50 preserve_state = False use_paging = True def build_initial_query( self, session ): return session.query( self.model_class ) - def apply_default_filter( self, trans, query, **kwargs ): + def apply_default_filter( self, trans, query, **kwd ): return query.filter( self.model_class.deleted==False ) -class ToolBrowserController( BaseController ): - - tool_category_list_grid = ToolCategoryListGrid() +class ToolController( BaseController ): + tool_list_grid = ToolListGrid() + tools_by_user_list_grid = ToolsByUserListGrid() + category_list_grid = CategoryListGrid() @web.expose def index( self, trans, **kwd ): @@ -188,53 +296,84 @@ status = params.get( 'status', 'done' ) return trans.fill_template( '/webapps/community/index.mako', message=message, status=status ) @web.expose - def browse_tool_categories( self, trans, **kwargs ): - if 'operation' in kwargs: - operation = kwargs['operation'].lower() + def browse_categories( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() if operation == "browse category": - category_id = int( trans.app.security.decode_id( kwargs['id'] ) ) - category = trans.sa_session.query( model.Category ).get( category_id ) - del kwargs['id'] - del kwargs['operation'] - kwargs['f-category'] = category.name - return trans.response.send_redirect( web.url_for( controller='tool', - action='browse_tools', - **kwargs ) ) - return self.tool_category_list_grid( trans, **kwargs ) + return self.browse_category( trans, id=kwd['id'] ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='view_category', + cntrller='tool', + **kwd ) ) + elif operation == "edit tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_category', + cntrller='tool', + **kwd ) ) + # Render the list view + return self.category_list_grid( trans, **kwd ) @web.expose - def browse_tools( self, trans, **kwargs ): - if 'operation' in kwargs: - operation = kwargs['operation'].lower() - if operation == "browse": - return trans.response.send_redirect( web.url_for( controller='tool', - action='browse_tool', + def browse_category( self, trans, **kwd ): + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='tool', + **kwd ) ) + @web.expose + def browse_tools( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "browse category": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', cntrller='tool', - **kwargs ) ) + **kwd ) ) elif operation == "view tool": return trans.response.send_redirect( web.url_for( controller='common', action='view_tool', cntrller='tool', - **kwargs ) ) + **kwd ) ) elif operation == "edit tool": return trans.response.send_redirect( web.url_for( controller='common', action='edit_tool', cntrller='tool', - **kwargs ) ) + **kwd ) ) elif operation == "download tool": return trans.response.send_redirect( web.url_for( controller='tool', action='download_tool', - **kwargs ) ) + **kwd ) ) # Render the list view - return self.tool_list_grid( trans, **kwargs ) + return self.tool_list_grid( trans, **kwd ) @web.expose - def browse_tool( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - return trans.fill_template( '/webapps/community/tool/browse_tool.mako', - tools=tools, - message=message, - status=status ) + def browse_tools_by_user( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "browse": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_tools_by_user', + cntrller='tool', + **kwd ) ) + elif operation == "browse category": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='tool', + **kwd ) ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='view_tool', + cntrller='tool', + **kwd ) ) + elif operation == "edit tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_tool', + cntrller='tool', + **kwd ) ) + elif operation == "download tool": + return trans.response.send_redirect( web.url_for( controller='tool', + action='download_tool', + **kwd ) ) + # Render the list view + return self.tools_by_user_list_grid( trans, **kwd ) @web.expose def download_tool( self, trans, **kwd ): params = util.Params( kwd ) diff -r c642fbb301fc -r db4f8befcd89 lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py Fri Apr 30 13:09:29 2010 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Fri Apr 30 14:08:23 2010 -0400 @@ -92,7 +92,8 @@ DELETED = 'deleted', WAITING = 'waiting for approval', APPROVED = 'approved', - REJECTED = 'rejected' ) + REJECTED = 'rejected', + ARCHIVED = 'archived' ) def __init__( self, guid=None, tool_id=None, name=None, description=None, user_description=None, category=None, version=None, user_id=None, external_filename=None ): self.guid = guid self.tool_id = tool_id @@ -153,10 +154,14 @@ return self.state() == self.states.ERROR def is_deleted( self ): return self.state() == self.states.DELETED + def is_waiting( self ): + return self.state() == self.states.WAITING def is_approved( self ): return self.state() == self.states.APPROVED def is_rejected( self ): return self.state() == self.states.REJECTED + def is_archived( self ): + return self.state() == self.states.ARCHIVED @property def extension( self ): # if instantiated via a query, this unmapped property won't exist diff -r c642fbb301fc -r db4f8befcd89 lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py Fri Apr 30 13:09:29 2010 -0400 +++ b/lib/galaxy/webapps/community/model/mapping.py Fri Apr 30 14:08:23 2010 -0400 @@ -164,8 +164,8 @@ # With the tables defined we can define the mappers and setup the # relationships between the model objects. assign_mapper( context, User, User.table, - properties=dict( tools=relation( Tool, order_by=desc( Tool.table.c.update_time ) ), - active_tools=relation( Tool, primaryjoin=( ( Tool.table.c.user_id == User.table.c.id ) & ( not_( Tool.table.c.deleted ) ) ), order_by=desc( Tool.table.c.update_time ) ), + properties=dict( tools=relation( Tool, primaryjoin=( Tool.table.c.user_id == User.table.c.id ), order_by=( Tool.table.c.name ) ), + active_tools=relation( Tool, primaryjoin=( ( Tool.table.c.user_id == User.table.c.id ) & ( not_( Tool.table.c.deleted ) ) ), order_by=( Tool.table.c.name ) ), galaxy_sessions=relation( GalaxySession, order_by=desc( GalaxySession.table.c.update_time ) ) ) ) assign_mapper( context, Group, Group.table, @@ -238,7 +238,6 @@ ) ) - def guess_dialect_for_url( url ): return (url.split(':', 1))[0] diff -r c642fbb301fc -r db4f8befcd89 templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako Fri Apr 30 13:09:29 2010 -0400 +++ b/templates/webapps/community/admin/index.mako Fri Apr 30 14:08:23 2010 -0400 @@ -54,7 +54,6 @@ </style> </%def> - <%def name="init()"> <% self.has_left_panel=True @@ -71,32 +70,34 @@ <div class="toolMenu"> <div class="toolSectionList"> <div class="toolSectionTitle"> + <span>Tools</span> + </div> + <div class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_tools_by_state', state=trans.model.Tool.states.WAITING, webapp='community' )}">Tools awaiting approval</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_tools_by_category' )}">Browse by category</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_tools', webapp='community' )}">Browse all tools</a></div> + </div> + </div> + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + <span>Categories</span> + </div> + <div class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='manage_categories', webapp='community' )}">Manage categories</a></div> + </div> + </div> + <div class="toolSectionTitle"> <span>Security</span> </div> <div class="toolSectionBody"> <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='users', webapp='community' )}" target="galaxy_main">Manage users</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='groups', webapp='community' )}" target="galaxy_main">Manage groups</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='roles', webapp='community' )}" target="galaxy_main">Manage roles</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='users', webapp='community' )}">Manage users</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='groups', webapp='community' )}">Manage groups</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='roles', webapp='community' )}">Manage roles</a></div> </div> </div> - <div class="toolSectionTitle"> - <span>Tools</span> - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tools', webapp='community' )}" target="galaxy_main">Manage tools</a></div> - </div> - </div> - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - <span>Community</span> - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='categories', webapp='community' )}" target="galaxy_main">Manage categories</a></div> - </div> - </div> </div> </div> </div> diff -r c642fbb301fc -r db4f8befcd89 templates/webapps/community/category/edit_category.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/category/edit_category.mako Fri Apr 30 14:08:23 2010 -0400 @@ -0,0 +1,44 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Change category name and description</div> + <div class="toolFormBody"> + <form name="library" action="${h.url_for( controller='admin', action='edit_category' )}" method="post" > + <div class="form-row"> + <input name="webapp" type="hidden" value="${webapp}" size=40"/> + <label>Name:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="text" name="name" value="${category.name}" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Description:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input name="description" type="textfield" value="${category.description}" size=40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="rename" value="submitted"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="id" value="${trans.security.encode_id( category.id )}"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="edit_category_button" value="Save"/> + </div> + </form> + </div> +</div> diff -r c642fbb301fc -r db4f8befcd89 templates/webapps/community/category/rename_category.mako --- a/templates/webapps/community/category/rename_category.mako Fri Apr 30 13:09:29 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Change category name and description</div> - <div class="toolFormBody"> - <form name="library" action="${h.url_for( controller='admin', action='rename_category' )}" method="post" > - <div class="form-row"> - <input name="webapp" type="hidden" value="${webapp}" size=40"/> - <label>Name:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${category.name}" size="40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Description:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input name="description" type="textfield" value="${category.description}" size=40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="rename" value="submitted"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="id" value="${trans.security.encode_id( category.id )}"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="rename_category_button" value="Save"/> - </div> - </form> - </div> -</div> diff -r c642fbb301fc -r db4f8befcd89 templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako Fri Apr 30 13:09:29 2010 -0400 +++ b/templates/webapps/community/index.mako Fri Apr 30 14:08:23 2010 -0400 @@ -1,6 +1,57 @@ <%inherit file="/webapps/community/base_panels.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<%def name="stylesheets()"> + ${parent.stylesheets()} + ## TODO: Clean up these styles and move into panel_layout.css (they are + ## used here and in the editor). + <style type="text/css"> + #left { + background: #C1C9E5 url(${h.url_for('/static/style/menu_bg.png')}) top repeat-x; + } + div.toolMenu { + margin: 5px; + margin-left: 10px; + margin-right: 10px; + } + div.toolSectionPad { + margin: 0; + padding: 0; + height: 5px; + font-size: 0px; + } + div.toolSectionDetailsInner { + margin-left: 5px; + margin-right: 5px; + } + div.toolSectionTitle { + padding-bottom: 0px; + font-weight: bold; + } + div.toolMenuGroupHeader { + font-weight: bold; + padding-top: 0.5em; + padding-bottom: 0.5em; + color: #333; + font-style: italic; + border-bottom: dotted #333 1px; + margin-bottom: 0.5em; + } + div.toolTitle { + padding-top: 5px; + padding-bottom: 5px; + margin-left: 16px; + margin-right: 10px; + display: list-item; + list-style: square outside; + } + a:link, a:visited, a:active + { + color: #303030; + } + </style> +</%def> + <%def name="init()"> <% self.has_left_panel=True @@ -29,17 +80,18 @@ </div> <div class="toolSectionBody"> <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='tool', action='browse_tool_categories' )}" target="galaxy_main">Browse tools by category</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='tool', action='browse_tools' )}" target="galaxy_main">Browse all tools</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_categories' )}">Browse by category</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_tools' )}">Browse all tools</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_tools_by_user', operation='browse', id=trans.security.encode_id( trans.user.id ) )}">Browse your tools</a></div> </div> </div> <div class="toolSectionBody"> <div class="toolSectionBg"> <div class="toolTitle"> %if trans.user: - <a href="${h.url_for( controller='upload', action='upload', type='tool' )}" target="galaxy_main">Upload a tool</a> + <a target="galaxy_main" href="${h.url_for( controller='upload', action='upload', type='tool' )}">Upload a tool</a> %else: - Login to upload + <a target="galaxy_main" href="${h.url_for( controller='/user', action='login', webapp='community' )}">Login to upload</a> %endif </div> </div> @@ -54,7 +106,7 @@ if trans.app.config.require_login and not trans.user: center_url = h.url_for( controller='user', action='login', message=message, status=status ) else: - center_url = h.url_for( controller='tool', action='browse_tool_categories', message=message, status=status ) + center_url = h.url_for( controller='tool', action='browse_categories', message=message, status=status ) %> <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"> </iframe> </%def> diff -r c642fbb301fc -r db4f8befcd89 templates/webapps/community/tool/browse_tool.mako --- a/templates/webapps/community/tool/browse_tool.mako Fri Apr 30 13:09:29 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -<%namespace file="/message.mako" import="render_msg" /> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/community/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="title()">Browse Tool</%def> - -<h2>Galaxy Tool</h2> - -%if message: - ${render_msg( message, status )} -%endif - -%if not tools: - There are no tools -%else: - <table class="grid"> - <thead> - <tr> - <th>Name</th> - <th>Description</th> - </tr> - </thead> - <tbody> - <tr class="formRow id="toolRow"> - <td><a href="${h.url_for( controller='tool', action='browse', id=trans.security.encode_id( tool.id ) )}">${tool.name}</a></td> - <td>${tool.description}</td> - </tr> - </tbody> - </table> -%endif diff -r c642fbb301fc -r db4f8befcd89 templates/webapps/community/tool/edit_tool.mako --- a/templates/webapps/community/tool/edit_tool.mako Fri Apr 30 13:09:29 2010 -0400 +++ b/templates/webapps/community/tool/edit_tool.mako Fri Apr 30 14:08:23 2010 -0400 @@ -123,7 +123,7 @@ <div class="toolParamHelp" style="clear: both;"> Tools must be approved before they are made available to others in the community. After you have submitted your tool to be published, you will no longer be able to modify it, so make sure the information above is - correct and has been saved before submitting for approval. + correct and and save any changes before submitting for approval. </div> </div> </form> diff -r c642fbb301fc -r db4f8befcd89 templates/webapps/community/tool/view_tool.mako --- a/templates/webapps/community/tool/view_tool.mako Fri Apr 30 13:09:29 2010 -0400 +++ b/templates/webapps/community/tool/view_tool.mako Fri Apr 30 14:08:23 2010 -0400 @@ -49,6 +49,14 @@ <h2>View Tool: ${tool.name} <em>${tool.description}</em></h2> +%if cntrller=='admin' and tool.is_waiting(): + <p> + <ul class="manage-table-actions"> + <li><a class="action-button" href="${h.url_for( controller='admin', action='set_tool_state', state=trans.model.Tool.states.APPROVED, id=trans.security.encode_id( tool.id ), cntrller=cntrller )}"><span>Approve</span></a></li> + </ul> + </p> +%endif + %if message: ${render_msg( message, status )} %endif

1 0

[hg] galaxy 3721: merge
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c642fbb301fc changeset: 3721:c642fbb301fc user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Apr 30 13:09:29 2010 -0400 description: merge diffstat: lib/galaxy/datatypes/interval.py | 5 +- lib/galaxy/web/base/controller.py | 12 +- lib/galaxy/web/controllers/dataset.py | 12 +- tools/ngs_rna/tophat_wrapper.py | 216 +++++++++++++++---- tools/ngs_rna/tophat_wrapper.xml | 364 +++++++++++++++++++++++++++++---- 5 files changed, 503 insertions(+), 106 deletions(-) diffs (733 lines): diff -r 20ba52b9d504 -r c642fbb301fc lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Fri Apr 30 13:08:33 2010 -0400 +++ b/lib/galaxy/datatypes/interval.py Fri Apr 30 13:09:29 2010 -0400 @@ -831,9 +831,12 @@ except: return False -class Gtf( Tabular ): +class Gtf( Gff ): """Tab delimited data in Gtf format""" file_ext = "gtf" + + def sniff( self, filename ): + return False class Wiggle( Tabular, _RemoteCallMixin ): """Tab delimited data in wiggle format""" diff -r 20ba52b9d504 -r c642fbb301fc lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py Fri Apr 30 13:08:33 2010 -0400 +++ b/lib/galaxy/web/base/controller.py Fri Apr 30 13:09:29 2010 -0400 @@ -122,10 +122,14 @@ """ Get an HDA object by id. """ # DEPRECATION: We still support unencoded ids for backward compatibility try: - dataset_id = int( dataset_id ) - except ValueError: - dataset_id = trans.security.decode_id( dataset_id ) - data = trans.sa_session.query( trans.model.HistoryDatasetAssociation ).get( dataset_id ) + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) + if data is None: + raise ValueError( 'Invalid reference dataset id: %s.' % dataset_id ) + except: + try: + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( int( dataset_id ) ) + except: + data = None if not data: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid dataset id: %s." % str( dataset_id ) ) if check_ownership: diff -r 20ba52b9d504 -r c642fbb301fc lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Fri Apr 30 13:08:33 2010 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Fri Apr 30 13:09:29 2010 -0400 @@ -307,10 +307,14 @@ composite_extensions.append('html') # for archiving composite datatypes # DEPRECATION: We still support unencoded ids for backward compatibility try: - dataset_id = int( dataset_id ) - except ValueError: - dataset_id = trans.security.decode_id( dataset_id ) - data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id ) + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) + if data is None: + raise ValueError( 'Invalid reference dataset id: %s.' % dataset_id ) + except: + try: + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( int( dataset_id ) ) + except: + data = None if not data: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) current_user_roles = trans.get_current_user_roles() diff -r 20ba52b9d504 -r c642fbb301fc tools/ngs_rna/tophat_wrapper.py --- a/tools/ngs_rna/tophat_wrapper.py Fri Apr 30 13:08:33 2010 -0400 +++ b/tools/ngs_rna/tophat_wrapper.py Fri Apr 30 13:09:29 2010 -0400 @@ -1,6 +1,6 @@ #!/usr/bin/env python -import optparse, os, shutil, sys, tempfile +import optparse, os, shutil, subprocess, sys, tempfile, fileinput def stop_err( msg ): sys.stderr.write( "%s\n" % msg ) @@ -9,72 +9,184 @@ def __main__(): #Parse Command Line parser = optparse.OptionParser() - parser.add_option( '-1', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' ) - parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' ) + parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' ) + parser.add_option( '-C', '--coverage-output', dest='coverage_output_file', help='Coverage output file; formate is WIG.' ) + parser.add_option( '-J', '--junctions-output', dest='junctions_output_file', help='Junctions output file; formate is BED.' ) + parser.add_option( '-H', '--hits-output', dest='accepted_hits_output_file', help='Accepted hits output file; formate is SAM.' ) + parser.add_option( '', '--own-file', dest='own_file', help='' ) + parser.add_option( '-D', '--indexes-path', dest='index_path', help='Indexes directory; location of .ebwt and .fa files.' ) + parser.add_option( '-r', '--mate-inner-dist', dest='mate_inner_dist', help='This is the expected (mean) inner distance between mate pairs. \ + For, example, for paired end runs with fragments selected at 300bp, \ + where each end is 50bp, you should set -r to be 200. There is no default, \ + and this parameter is required for paired end runs.') + parser.add_option( '', '--mate-std-dev', dest='mate_std_dev', help='Standard deviation of distribution on inner distances between male pairs.' ) parser.add_option( '-a', '--min-anchor-length', dest='min_anchor_length', help='The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction.' ) + parser.add_option( '-m', '--splice-mismatches', dest='splice_mismatches', help='The maximum number of mismatches that can appear in the anchor region of a spliced alignment.' ) parser.add_option( '-i', '--min-intron-length', dest='min_intron_length', help='The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart.' ) parser.add_option( '-I', '--max-intron-length', dest='max_intron_length', help='The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read.' ) - parser.add_option( '-s', '--solexa-quals', dest='solexa_quals', help='Use the Solexa scale for quality values in FASTQ files.' ) - parser.add_option( '-S', '--solexa.3-quals', dest='solexa_quals', - help='As of the Illumina GA pipeline version 1.3, quality scores are encoded in Phred-scaled base-64. Use this option for FASTQ files from pipeline 1.3 or later.' ) - parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' ) - parser.add_option( '-C', '--coverage-output', dest='coverage_output_file', help='Coverage output file; formate is WIG.' ) - parser.add_option( '-J', '--junctions-output', dest='junctions_output_file', help='Junctions output file; formate is BED.' ) - parser.add_option( '-H', '--hits-output', dest='accepted_hits_output_file', help='Accepted hits output file; formate is SAM.' ) - parser.add_option( '-D', '--indexes-dir', dest='indexes_directory', help='Indexes directory; location of .ebwt and .fa files.' ) - parser.add_option( '-r', '--mate-inner-dist', dest='mate_inner_dist', help='This is the expected (mean) inner distance between mate pairs. \ - For, example, for paired end runs with fragments selected at 300bp, \ - where each end is 50bp, you should set -r to be 200. There is no default, \ - and this parameter is required for paired end runs.') + parser.add_option( '-F', '--junction_filter', dest='junction_filter', help='Filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)' ) + parser.add_option( '-g', '--max_multihits', dest='max_multihits', help='Maximum number of alignments to be allowed' ) + parser.add_option( '', '--microexon-search', action="store_true", dest='microexon_search', help='With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.') + parser.add_option( '', '--closure-search', action="store_true", dest='closure_search', help='Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (<= 50bp)') + parser.add_option( '', '--no-closure-search', action="store_false", dest='closure_search' ) + parser.add_option( '', '--coverage-search', action="store_true", dest='coverage_search', help='Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.') + parser.add_option( '', '--no-coverage-search', action="store_false", dest='coverage_search' ) + parser.add_option( '', '--min-segment-intron', dest='min_segment_intron', help='Minimum intron length that may be found during split-segment search' ) + parser.add_option( '', '--max-segment-intron', dest='max_segment_intron', help='Maximum intron length that may be found during split-segment search' ) + parser.add_option( '', '--min-closure-exon', dest='min_closure_exon', help='Minimum length for exonic hops in potential splice graph' ) + parser.add_option( '', '--min-closure-intron', dest='min_closure_intron', help='Minimum intron length that may be found during closure search' ) + parser.add_option( '', '--max-closure-intron', dest='max_closure_intron', help='Maximum intron length that may be found during closure search' ) + parser.add_option( '', '--min-coverage-intron', dest='min_coverage_intron', help='Minimum intron length that may be found during coverage search' ) + parser.add_option( '', '--max-coverage-intron', dest='max_coverage_intron', help='Maximum intron length that may be found during coverage search' ) + parser.add_option( '', '--seg-mismatches', dest='seg_mismatches', help='Number of mismatches allowed in each segment alignment for reads mapped independently' ) + parser.add_option( '', '--seg-length', dest='seg_length', help='Minimum length of read segments' ) + + # Wrapper options. + parser.add_option( '-1', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' ) + parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' ) + parser.add_option( '', '--single-paired', dest='single_paired', help='' ) + parser.add_option( '', '--settings', dest='settings', help='' ) + (options, args) = parser.parse_args() - # Make temp directory for output. + #sys.stderr.write('*'*50+'\n'+str(options)+'\n'+'*'*50+'\n') + + # Creat bowtie index if necessary. + tmp_index_dir = tempfile.mkdtemp() + if options.own_file != 'None': + index_path = os.path.join( tmp_index_dir, os.path.split( options.own_file )[1] ) + cmd_index = 'bowtie-build -f %s %s' % ( options.own_file, index_path ) + try: + tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd_index, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + if returncode != 0: + raise Exception, stderr + except Exception, e: + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + stop_err( 'Error indexing reference sequence\n' + str( e ) ) + else: + index_path = options.index_path + + # Build tophat command. tmp_output_dir = tempfile.mkdtemp() - - # Build command. - - # Base. - cmd = "tophat -o %s " % ( tmp_output_dir ) - - # Add options. - if options.mate_inner_dist: - cmd += ( " -r %i" % int ( options.mate_inner_dist ) ) - - # Add index prefix. - cmd += " " + options.indexes_directory - - # Add input files. - cmd += " " + options.input1 - if options.mate_inner_dist: - # Using paired-end reads. - cmd += " " + options.input2 - - # Route program output to file. - cmd += " > %s" % tmp_output_dir + "/std_out.txt" - # Route program error output to file. - cmd += " 2> %s" % tmp_output_dir + "/std_err.txt" - - # Run. + cmd = 'tophat -o %s %s %s %s' + reads = options.input1 + if options.input2 != 'None': + reads += ' ' + options.input2 + opts = '-p %s' % options.num_threads + if options.single_paired == 'paired': + opts += ' -r %s' % options.mate_inner_dist + if options.settings == 'preSet': + cmd = cmd % ( tmp_output_dir, opts, index_path, reads ) + else: + try: + if int( options.min_anchor_length ) >= 3: + opts += ' -a %s' % options.min_anchor_length + else: + raise Exception, 'Minimum anchor length must be 3 or greater' + opts += ' -m %s' % options.splice_mismatches + opts += ' -i %s' % options.min_intron_length + opts += ' -I %s' % options.max_intron_length + if float( options.junction_filter ) != 0.0: + opts += ' -F %s' % options.junction_filter + opts += ' -g %s' % options.max_multihits + if options.coverage_search: + opts += ' --coverage-search --min-coverage-intron %s --max-coverage-intron %s' % ( options.min_coverage_intron, options.max_coverage_intron ) + else: + opts += ' --no-coverage-search' + if options.closure_search: + opts += ' --closure-search --min-closure-exon %s --min-closure-intron %s --max-closure-intron %s' % ( options.min_closure_exon, options.min_closure_intron, options.max_closure_intron ) + else: + opts += ' --no-closure-search' + if options.microexon_search: + opts += ' --microexon-search' + if options.single_paired == 'paired': + opts += ' --mate-std-dev %s' % options.mate_std_dev + cmd = cmd % ( tmp_output_dir, opts, index_path, reads ) + except Exception, e: + # Clean up temp dirs + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + if os.path.exists( tmp_output_dir ): + shutil.rmtree( tmp_output_dir ) + stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) ) + print cmd + + # Run try: - os.system( cmd ) + tmp_out = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name + tmp_stdout = open( tmp_out, 'wb' ) + tmp_err = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name + tmp_stderr = open( tmp_err, 'wb' ) + proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_output_dir, stdout=tmp_stdout, stderr=tmp_stderr ) + returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp_err, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stdout.close() + tmp_stderr.close() + if returncode != 0: + raise Exception, stderr except Exception, e: + # Clean up temp dirs + if os.path.exists( tmp_output_dir ): + shutil.rmtree( tmp_output_dir ) stop_err( 'Error in tophat:\n' + str( e ) ) # TODO: look for errors in program output. - # Copy output files from tmp directory to specified files. + # Postprocessing: copy output files from tmp directory to specified files. Also need to remove header lines from SAM file. try: - shutil.copyfile( tmp_output_dir + "/coverage.wig", options.coverage_output_file ) - shutil.copyfile( tmp_output_dir + "/junctions.bed", options.junctions_output_file ) - shutil.copyfile( tmp_output_dir + "/accepted_hits.sam", options.accepted_hits_output_file ) - except Exception, e: - stop_err( 'Error in tophat:\n' + str( e ) ) - - # Clean up temp dirs - if os.path.exists( tmp_output_dir ): - shutil.rmtree( tmp_output_dir ) + try: + shutil.copyfile( tmp_output_dir + "/coverage.wig", options.coverage_output_file ) + shutil.copyfile( tmp_output_dir + "/junctions.bed", options.junctions_output_file ) + + # Remove headers from SAM file in place. + in_header = True # Headers always at start of file. + for line in fileinput.input( tmp_output_dir + "/accepted_hits.sam", inplace=1 ): + if in_header and line.startswith("@"): + continue + else: + in_header = False + sys.stdout.write( line ) + + # Copy SAM File. + shutil.copyfile( tmp_output_dir + "/accepted_hits.sam", options.accepted_hits_output_file ) + except Exception, e: + stop_err( 'Error in tophat:\n' + str( e ) ) + finally: + # Clean up temp dirs + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + if os.path.exists( tmp_output_dir ): + shutil.rmtree( tmp_output_dir ) if __name__=="__main__": __main__() diff -r 20ba52b9d504 -r c642fbb301fc tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml Fri Apr 30 13:08:33 2010 -0400 +++ b/tools/ngs_rna/tophat_wrapper.xml Fri Apr 30 13:09:29 2010 -0400 @@ -1,24 +1,104 @@ -<tool id="tophat" name="Tophat" version="1.0.13"> +<tool id="tophat" name="Tophat" version="1.0.0"> <description>Find splice junctions using RNA-seq data</description> <command interpreter="python"> - tophat_wrapper.py + tophat_wrapper.py + ## Change this to accomodate the number of threads you have available. --num-threads="4" - --coverage-output=$coverage - --junctions-output=$junctions + + ## Provide outputs. + --coverage-output=$coverage + --junctions-output=$junctions --hits-output=$accepted_hits + + ## Handle reference file. #if $refGenomeSource.genomeSource == "history": - --indexes-dir=$refGenomeSource.ownFile + --own-file=$refGenomeSource.ownFile + --indexes-path="None" #else: - --indexes-dir=$refGenomeSource.index.value + --own-file="None" + --indexes-path=$refGenomeSource.index.value #end if + + ## Are reads single-end or paired? + --single-paired=$singlePaired.sPaired + + ## First input file always required. + --input1=$singlePaired.input1 + + ## Set parms based on whether reads are single-end or paired. #if $singlePaired.sPaired == "single": - --input1=$singlePaired.input1 --input2="None" - #else: - -r $singlePaired.mean_inner_distance - --input1=$singlePaired.input1 - --input2=$singlePaired.input2 - #end if + -r "None" + --settings=$singlePaired.sParams.sSettingsType + #if $singlePaired.sParams.sSettingsType == "full": + --mate-std-dev="None" + -a $singlePaired.sParams.anchor_length + -m $singlePaired.sParams.splice_mismatches + -i $singlePaired.sParams.min_intron_length + -I $singlePaired.sParams.max_intron_length + -F $singlePaired.sParams.junction_filter + -g $singlePaired.sParams.max_multihits + --min-segment-intron $singlePaired.sParams.min_segment_intron + --max-segment-intron $singlePaired.sParams.max_segment_intron + --seg-mismatches=$singlePaired.sParams.seg_mismatches + --seg-length=$singlePaired.sParams.seg_length + #if $singlePaired.sParams.closure_search.use_search == "Yes": + --closure-search + --min-closure-exon $singlePaired.sParams.closure_search.min_closure_exon + --min-closure-intron $singlePaired.sParams.closure_search.min_closure_intron + --max-closure-intron $singlePaired.sParams.closure_search.max_closure_intron + #else: + --no-closure-search + #end if + #if $singlePaired.sParams.coverage_search.use_search == "Yes": + --coverage-search + --min-coverage-intron $singlePaired.sParams.coverage_search.min_coverage_intron + --max-coverage-intron $singlePaired.sParams.coverage_search.max_coverage_intron + #else: + --no-coverage-search + #end if + ## No idea why the type conversion is necessary, but it seems to be. + #if str ($singlePaired.sParams.microexon_search) == "Yes": + --microexon-search + #end if + #end if + #else: + --input2=$singlePaired.input2 + -r $singlePaired.mate_inner_distance + --settings=$singlePaired.pParams.pSettingsType + #if $singlePaired.pParams.pSettingsType == "full": + --mate-std-dev=$singlePaired.pParams.mate_std_dev + -a $singlePaired.pParams.anchor_length + -m $singlePaired.pParams.splice_mismatches + -i $singlePaired.pParams.min_intron_length + -I $singlePaired.pParams.max_intron_length + -F $singlePaired.pParams.junction_filter + -g $singlePaired.pParams.max_multihits + --min-segment-intron $singlePaired.pParams.min_segment_intron + --max-segment-intron $singlePaired.pParams.max_segment_intron + --seg-mismatches=$singlePaired.pParams.seg_mismatches + --seg-length=$singlePaired.pParams.seg_length + #if $singlePaired.pParams.closure_search.use_search == "Yes": + --closure-search + --min-closure-exon $singlePaired.pParams.closure_search.min_closure_exon + --min-closure-intron $singlePaired.pParams.closure_search.min_closure_intron + --max-closure-intron $singlePaired.pParams.closure_search.max_closure_intron + #else: + --no-closure-search + #end if + #if $singlePaired.pParams.coverage_search.use_search == "Yes": + --coverage-search + --min-coverage-intron $singlePaired.pParams.coverage_search.min_coverage_intron + --max-coverage-intron $singlePaired.pParams.coverage_search.max_coverage_intron + #else: + --no-coverage-search + #end if + ## No idea why the type conversion is necessary, but it seems to be. + #if str ($singlePaired.pParams.microexon_search) == "Yes": + --microexon-search + #end if + #end if + #end if </command> <inputs> <conditional name="refGenomeSource"> @@ -27,56 +107,219 @@ <option value="history">Use one from the history</option> </param> <when value="indexed"> - <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_file="bowtie_indices.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> - </param> - </when> + <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> + <options from_file="bowtie_indices.loc"> + <column name="value" index="1" /> + <column name="name" index="0" /> + </options> + </param> + </when> <when value="history"> <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> </when>  - </conditional>  + </conditional>  <conditional name="singlePaired"> <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> </param> <when value="single"> - <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <conditional name="sParams"> + <param name="sSettingsType" type="select" label="TopHat settings to use" help="You can use the default settings or set custom values for any of Tophat's parameters."> + <option value="preSet">Use Defaults</option> + <option value="full">Full parameter list</option> + </param> + <when value="preSet" /> +  + <when value="full"> + <param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." /> + <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" /> + <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." /> + <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /> + <param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" /> + <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /> + <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /> + <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" /> + <param name="seg_mismatches" type="integer" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /> + <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /> +  + <conditional name="closure_search"> + <param name="use_search" type="select" label="Use Closure Search"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param name="min_closure_exon" type="integer" value="50" label="During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50." /> + <param name="min_closure_intron" type="integer" value="50" label="Minimum intron length that may be found during closure search" /> + <param name="max_closure_intron" type="integer" value="5000" label="Maximum intron length that may be found during closure search" /> + </when> + <when value="No" /> + </conditional> +  + <conditional name="coverage_search"> + <param name="use_search" type="select" label="Use Coverage Search"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" /> + <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" /> + </when> + <when value="No" /> + </conditional> + <param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer."> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + </when>  + </conditional>  </when> <when value="paired"> - <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> - <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> - <param format="fastqsanger" name="mean_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs"/> + <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="mate_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs" /> + <conditional name="pParams"> + <param name="pSettingsType" type="select" label="TopHat settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> + <option value="preSet">Commonly used</option> + <option value="full">Full parameter list</option> + </param> + <when value="preSet" /> +  + <when value="full"> + <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/> + <param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." /> + <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" /> + <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." /> + <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /> + <param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" /> + <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /> + <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /> + <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" /> + <param name="seg_mismatches" type="integer" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /> + <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /> +  + <conditional name="closure_search"> + <param name="use_search" type="select" label="Use Closure Search"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param name="min_closure_exon" type="integer" value="50" label="During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50." /> + <param name="min_closure_intron" type="integer" value="50" label="Minimum intron length that may be found during closure search" /> + <param name="max_closure_intron" type="integer" value="5000" label="Maximum intron length that may be found during closure search" /> + </when> + <when value="No" /> + </conditional> +  + <conditional name="coverage_search"> + <param name="use_search" type="select" label="Use Coverage Search"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" /> + <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" /> + </when> + <when value="No" /> + </conditional> + <param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer."> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + </when>  + </conditional>  </when> </conditional> </inputs> - + <outputs> - <data format="sam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/> - <data format="wig" name="coverage" label="${tool.name} on ${on_string}: coverage"/> + <data format="sam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/> + <data format="bedgraph" name="coverage" label="${tool.name} on ${on_string}: coverage"/> <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"/> </outputs> - + <tests> +  + +  <test> - <param name="genomeSource" value="indexed"/> - <param name="index" value="test_ref"/> + <param name="genomeSource" value="history"/> + <param name="ownFile" ftype="fasta" value="tophat_in3.fa"/> <param name="sPaired" value="paired"/> <param name="input1" ftype="fastqsanger" value="tophat_in1.fq"/> <param name="input2" ftype="fastqsanger" value="tophat_in2.fq"/> - <param name="mean_inner_distance" value="20"/> -  <output name="coverage" file="tophat_out2.wig"/> <output name="junctions" file="tophat_out3.bed"/> </test> - </tests> - +  +  + </tests> + <help> **Tophat Overview** @@ -104,11 +347,15 @@ **Outputs** -Tophat produces three output files:: +Tophat produces three output files: - coverage.wig -- coverage of reads - accepted_hits.sam -- reads that were mapped onto genome - junctions.bed -- splice junctions identified by Tophat +- coverage.wig -- A UCSC BedGraph_ wigglegram track, showing the depth of coverage at each position, including the spliced read alignments. +- accepted_hits.sam -- A list of read alignments in SAM_ format. +- junctions.bed -- A UCSC BED_ track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction. + +.. _BedGraph: http://genome.ucsc.edu/goldenPath/help/bedgraph.html +.. _SAM: http://samtools.sourceforge.net/ +.. _BED: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 ------- @@ -122,8 +369,35 @@ This is a list of implemented Tophat options:: - -r This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments - selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter - is required for paired end runs. + -r This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments + selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter + is required for paired end runs. + --mate-std-dev INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp. + -a/--min-anchor-length INT The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction. Note that individual spliced + alignments may span a junction with fewer than this many bases on one side. However, every junction involved in spliced alignments is supported by at least one + read with this many bases on each side. This must be at least 3 and the default is 8. + -m/--splice-mismatches INT The maximum number of mismatches that may appear in the "anchor" region of a spliced alignment. The default is 0. + -i/--min-intron-length INT The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart. The default is 70. + -I/--max-intron-length INT The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read. The default is 500000. + -F/--min-isoform-fraction 0.0-1.0 TopHat filters out junctions supported by too few alignments. Suppose a junction spanning two exons, is supported by S reads. Let the average depth of coverage of + exon A be D, and assume that it is higher than B. If S / D is less than the minimum isoform fraction, the junction is not reported. A value of zero disables the + filter. The default is 0.15. + -g/--max-multihits INT Instructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many + alignments. The default is 40. + --no-closure-search Disables the mate pair closure-based search for junctions. Currently, has no effect - closure search is off by default. + --closure-search Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (about or less than 50bp) + --no-coverage-search Disables the coverage based search for junctions. + --coverage-search Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity. + --microexon-search With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer. + --butterfly-search TopHat will use a slower but potentially more sensitive algorithm to find junctions in addition to its standard search. Consider using this if you expect that your experiment produced a lot of reads from pre-mRNA, that fall within the introns of your transcripts. + --segment-mismatches Read segments are mapped independently, allowing up to this many mismatches in each segment alignment. The default is 2. + --segment-length Each read is cut up into segments, each at least this long. These segments are mapped independently. The default is 25. + --min-closure-exon During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50. + --min-closure-intron The minimum intron length that may be found during closure search. The default is 50. + --max-closure-intron The maximum intron length that may be found during closure search. The default is 5000. + --min-coverage-intron The minimum intron length that may be found during coverage search. The default is 50. + --max-coverage-intron The maximum intron length that may be found during coverage search. The default is 20000. + --min-segment-intron The minimum intron length that may be found during split-segment search. The default is 50. + --max-segment-intron The maximum intron length that may be found during split-segment search. The default is 500000. </help> </tool>

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[hg] galaxy 3720: Remove headers from SAM file so that output ma...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/20ba52b9d504 changeset: 3720:20ba52b9d504 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Apr 30 13:08:33 2010 -0400 description: Remove headers from SAM file so that output matches new Tophat wrapper. diffstat: test-data/tophat_out1.sam | 2 -- 1 files changed, 0 insertions(+), 2 deletions(-) diffs (9 lines): diff -r 436c9d1c5e64 -r 20ba52b9d504 test-data/tophat_out1.sam --- a/test-data/tophat_out1.sam Wed Apr 28 17:35:02 2010 -0400 +++ b/test-data/tophat_out1.sam Fri Apr 30 13:08:33 2010 -0400 @@ -1,5 +1,3 @@ -@HD VN:1.0 SO:sorted -@PG TopHat VN:1.0.13 CL:/Users/jeremy/projects/bx_tools/tophat-1.0.13/bin/tophat -r 20 test_ref reads_1.fq reads_2.fq test_mRNA_3_187_51 99 test_chromosome 53 255 75M = 163 0 TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 test_mRNA_4_191_5d 163 test_chromosome 54 255 75M = 167 0 ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 test_mRNA_5_197_46 97 test_chromosome 55 255 75M = 173 0 CTATCTGACTAGACTCGAGGCGCTTGCGTCTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2

1 0

[hg] galaxy 3719: Make GTF type subclass from GFF type.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/34c3789c86ef changeset: 3719:34c3789c86ef user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Apr 30 12:34:48 2010 -0400 description: Make GTF type subclass from GFF type. diffstat: lib/galaxy/datatypes/interval.py | 5 ++++- 1 files changed, 4 insertions(+), 1 deletions(-) diffs (17 lines): diff -r 853046b87a5c -r 34c3789c86ef lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Fri Apr 30 10:15:42 2010 -0400 +++ b/lib/galaxy/datatypes/interval.py Fri Apr 30 12:34:48 2010 -0400 @@ -831,9 +831,12 @@ except: return False -class Gtf( Tabular ): +class Gtf( Gff ): """Tab delimited data in Gtf format""" file_ext = "gtf" + + def sniff( self, filename ): + return False class Wiggle( Tabular, _RemoteCallMixin ): """Tab delimited data in wiggle format"""

1 0

[hg] galaxy 3718: Fix for backwards compatibility of HDAs being ...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/853046b87a5c changeset: 3718:853046b87a5c user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Apr 30 10:15:42 2010 -0400 description: Fix for backwards compatibility of HDAs being referenced as an integer. A hash that happened to be an integer would previously cause error. diffstat: lib/galaxy/web/base/controller.py | 12 ++++++++---- lib/galaxy/web/controllers/dataset.py | 12 ++++++++---- 2 files changed, 16 insertions(+), 8 deletions(-) diffs (44 lines): diff -r c09a8456b63e -r 853046b87a5c lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py Thu Apr 29 19:57:00 2010 -0400 +++ b/lib/galaxy/web/base/controller.py Fri Apr 30 10:15:42 2010 -0400 @@ -122,10 +122,14 @@ """ Get an HDA object by id. """ # DEPRECATION: We still support unencoded ids for backward compatibility try: - dataset_id = int( dataset_id ) - except ValueError: - dataset_id = trans.security.decode_id( dataset_id ) - data = trans.sa_session.query( trans.model.HistoryDatasetAssociation ).get( dataset_id ) + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) + if data is None: + raise ValueError( 'Invalid reference dataset id: %s.' % dataset_id ) + except: + try: + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( int( dataset_id ) ) + except: + data = None if not data: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid dataset id: %s." % str( dataset_id ) ) if check_ownership: diff -r c09a8456b63e -r 853046b87a5c lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Thu Apr 29 19:57:00 2010 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Fri Apr 30 10:15:42 2010 -0400 @@ -307,10 +307,14 @@ composite_extensions.append('html') # for archiving composite datatypes # DEPRECATION: We still support unencoded ids for backward compatibility try: - dataset_id = int( dataset_id ) - except ValueError: - dataset_id = trans.security.decode_id( dataset_id ) - data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id ) + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) + if data is None: + raise ValueError( 'Invalid reference dataset id: %s.' % dataset_id ) + except: + try: + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( int( dataset_id ) ) + except: + data = None if not data: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) current_user_roles = trans.get_current_user_roles()

1 0

[hg] galaxy 3717: Full Tophat wrapper. All options are implement...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c09a8456b63e changeset: 3717:c09a8456b63e user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Apr 29 19:57:00 2010 -0400 description: Full Tophat wrapper. All options are implemented, but additional tests are needed. diffstat: tools/ngs_rna/tophat_wrapper.py | 216 +++++++++++++++++----- tools/ngs_rna/tophat_wrapper.xml | 364 ++++++++++++++++++++++++++++++++++---- 2 files changed, 483 insertions(+), 97 deletions(-) diffs (672 lines): diff -r 436c9d1c5e64 -r c09a8456b63e tools/ngs_rna/tophat_wrapper.py --- a/tools/ngs_rna/tophat_wrapper.py Wed Apr 28 17:35:02 2010 -0400 +++ b/tools/ngs_rna/tophat_wrapper.py Thu Apr 29 19:57:00 2010 -0400 @@ -1,6 +1,6 @@ #!/usr/bin/env python -import optparse, os, shutil, sys, tempfile +import optparse, os, shutil, subprocess, sys, tempfile, fileinput def stop_err( msg ): sys.stderr.write( "%s\n" % msg ) @@ -9,72 +9,184 @@ def __main__(): #Parse Command Line parser = optparse.OptionParser() - parser.add_option( '-1', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' ) - parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' ) + parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' ) + parser.add_option( '-C', '--coverage-output', dest='coverage_output_file', help='Coverage output file; formate is WIG.' ) + parser.add_option( '-J', '--junctions-output', dest='junctions_output_file', help='Junctions output file; formate is BED.' ) + parser.add_option( '-H', '--hits-output', dest='accepted_hits_output_file', help='Accepted hits output file; formate is SAM.' ) + parser.add_option( '', '--own-file', dest='own_file', help='' ) + parser.add_option( '-D', '--indexes-path', dest='index_path', help='Indexes directory; location of .ebwt and .fa files.' ) + parser.add_option( '-r', '--mate-inner-dist', dest='mate_inner_dist', help='This is the expected (mean) inner distance between mate pairs. \ + For, example, for paired end runs with fragments selected at 300bp, \ + where each end is 50bp, you should set -r to be 200. There is no default, \ + and this parameter is required for paired end runs.') + parser.add_option( '', '--mate-std-dev', dest='mate_std_dev', help='Standard deviation of distribution on inner distances between male pairs.' ) parser.add_option( '-a', '--min-anchor-length', dest='min_anchor_length', help='The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction.' ) + parser.add_option( '-m', '--splice-mismatches', dest='splice_mismatches', help='The maximum number of mismatches that can appear in the anchor region of a spliced alignment.' ) parser.add_option( '-i', '--min-intron-length', dest='min_intron_length', help='The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart.' ) parser.add_option( '-I', '--max-intron-length', dest='max_intron_length', help='The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read.' ) - parser.add_option( '-s', '--solexa-quals', dest='solexa_quals', help='Use the Solexa scale for quality values in FASTQ files.' ) - parser.add_option( '-S', '--solexa.3-quals', dest='solexa_quals', - help='As of the Illumina GA pipeline version 1.3, quality scores are encoded in Phred-scaled base-64. Use this option for FASTQ files from pipeline 1.3 or later.' ) - parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' ) - parser.add_option( '-C', '--coverage-output', dest='coverage_output_file', help='Coverage output file; formate is WIG.' ) - parser.add_option( '-J', '--junctions-output', dest='junctions_output_file', help='Junctions output file; formate is BED.' ) - parser.add_option( '-H', '--hits-output', dest='accepted_hits_output_file', help='Accepted hits output file; formate is SAM.' ) - parser.add_option( '-D', '--indexes-dir', dest='indexes_directory', help='Indexes directory; location of .ebwt and .fa files.' ) - parser.add_option( '-r', '--mate-inner-dist', dest='mate_inner_dist', help='This is the expected (mean) inner distance between mate pairs. \ - For, example, for paired end runs with fragments selected at 300bp, \ - where each end is 50bp, you should set -r to be 200. There is no default, \ - and this parameter is required for paired end runs.') + parser.add_option( '-F', '--junction_filter', dest='junction_filter', help='Filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)' ) + parser.add_option( '-g', '--max_multihits', dest='max_multihits', help='Maximum number of alignments to be allowed' ) + parser.add_option( '', '--microexon-search', action="store_true", dest='microexon_search', help='With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.') + parser.add_option( '', '--closure-search', action="store_true", dest='closure_search', help='Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (<= 50bp)') + parser.add_option( '', '--no-closure-search', action="store_false", dest='closure_search' ) + parser.add_option( '', '--coverage-search', action="store_true", dest='coverage_search', help='Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.') + parser.add_option( '', '--no-coverage-search', action="store_false", dest='coverage_search' ) + parser.add_option( '', '--min-segment-intron', dest='min_segment_intron', help='Minimum intron length that may be found during split-segment search' ) + parser.add_option( '', '--max-segment-intron', dest='max_segment_intron', help='Maximum intron length that may be found during split-segment search' ) + parser.add_option( '', '--min-closure-exon', dest='min_closure_exon', help='Minimum length for exonic hops in potential splice graph' ) + parser.add_option( '', '--min-closure-intron', dest='min_closure_intron', help='Minimum intron length that may be found during closure search' ) + parser.add_option( '', '--max-closure-intron', dest='max_closure_intron', help='Maximum intron length that may be found during closure search' ) + parser.add_option( '', '--min-coverage-intron', dest='min_coverage_intron', help='Minimum intron length that may be found during coverage search' ) + parser.add_option( '', '--max-coverage-intron', dest='max_coverage_intron', help='Maximum intron length that may be found during coverage search' ) + parser.add_option( '', '--seg-mismatches', dest='seg_mismatches', help='Number of mismatches allowed in each segment alignment for reads mapped independently' ) + parser.add_option( '', '--seg-length', dest='seg_length', help='Minimum length of read segments' ) + + # Wrapper options. + parser.add_option( '-1', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' ) + parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' ) + parser.add_option( '', '--single-paired', dest='single_paired', help='' ) + parser.add_option( '', '--settings', dest='settings', help='' ) + (options, args) = parser.parse_args() - # Make temp directory for output. + #sys.stderr.write('*'*50+'\n'+str(options)+'\n'+'*'*50+'\n') + + # Creat bowtie index if necessary. + tmp_index_dir = tempfile.mkdtemp() + if options.own_file != 'None': + index_path = os.path.join( tmp_index_dir, os.path.split( options.own_file )[1] ) + cmd_index = 'bowtie-build -f %s %s' % ( options.own_file, index_path ) + try: + tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd_index, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + if returncode != 0: + raise Exception, stderr + except Exception, e: + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + stop_err( 'Error indexing reference sequence\n' + str( e ) ) + else: + index_path = options.index_path + + # Build tophat command. tmp_output_dir = tempfile.mkdtemp() - - # Build command. - - # Base. - cmd = "tophat -o %s " % ( tmp_output_dir ) - - # Add options. - if options.mate_inner_dist: - cmd += ( " -r %i" % int ( options.mate_inner_dist ) ) - - # Add index prefix. - cmd += " " + options.indexes_directory - - # Add input files. - cmd += " " + options.input1 - if options.mate_inner_dist: - # Using paired-end reads. - cmd += " " + options.input2 - - # Route program output to file. - cmd += " > %s" % tmp_output_dir + "/std_out.txt" - # Route program error output to file. - cmd += " 2> %s" % tmp_output_dir + "/std_err.txt" - - # Run. + cmd = 'tophat -o %s %s %s %s' + reads = options.input1 + if options.input2 != 'None': + reads += ' ' + options.input2 + opts = '-p %s' % options.num_threads + if options.single_paired == 'paired': + opts += ' -r %s' % options.mate_inner_dist + if options.settings == 'preSet': + cmd = cmd % ( tmp_output_dir, opts, index_path, reads ) + else: + try: + if int( options.min_anchor_length ) >= 3: + opts += ' -a %s' % options.min_anchor_length + else: + raise Exception, 'Minimum anchor length must be 3 or greater' + opts += ' -m %s' % options.splice_mismatches + opts += ' -i %s' % options.min_intron_length + opts += ' -I %s' % options.max_intron_length + if float( options.junction_filter ) != 0.0: + opts += ' -F %s' % options.junction_filter + opts += ' -g %s' % options.max_multihits + if options.coverage_search: + opts += ' --coverage-search --min-coverage-intron %s --max-coverage-intron %s' % ( options.min_coverage_intron, options.max_coverage_intron ) + else: + opts += ' --no-coverage-search' + if options.closure_search: + opts += ' --closure-search --min-closure-exon %s --min-closure-intron %s --max-closure-intron %s' % ( options.min_closure_exon, options.min_closure_intron, options.max_closure_intron ) + else: + opts += ' --no-closure-search' + if options.microexon_search: + opts += ' --microexon-search' + if options.single_paired == 'paired': + opts += ' --mate-std-dev %s' % options.mate_std_dev + cmd = cmd % ( tmp_output_dir, opts, index_path, reads ) + except Exception, e: + # Clean up temp dirs + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + if os.path.exists( tmp_output_dir ): + shutil.rmtree( tmp_output_dir ) + stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) ) + print cmd + + # Run try: - os.system( cmd ) + tmp_out = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name + tmp_stdout = open( tmp_out, 'wb' ) + tmp_err = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name + tmp_stderr = open( tmp_err, 'wb' ) + proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_output_dir, stdout=tmp_stdout, stderr=tmp_stderr ) + returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp_err, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stdout.close() + tmp_stderr.close() + if returncode != 0: + raise Exception, stderr except Exception, e: + # Clean up temp dirs + if os.path.exists( tmp_output_dir ): + shutil.rmtree( tmp_output_dir ) stop_err( 'Error in tophat:\n' + str( e ) ) # TODO: look for errors in program output. - # Copy output files from tmp directory to specified files. + # Postprocessing: copy output files from tmp directory to specified files. Also need to remove header lines from SAM file. try: - shutil.copyfile( tmp_output_dir + "/coverage.wig", options.coverage_output_file ) - shutil.copyfile( tmp_output_dir + "/junctions.bed", options.junctions_output_file ) - shutil.copyfile( tmp_output_dir + "/accepted_hits.sam", options.accepted_hits_output_file ) - except Exception, e: - stop_err( 'Error in tophat:\n' + str( e ) ) - - # Clean up temp dirs - if os.path.exists( tmp_output_dir ): - shutil.rmtree( tmp_output_dir ) + try: + shutil.copyfile( tmp_output_dir + "/coverage.wig", options.coverage_output_file ) + shutil.copyfile( tmp_output_dir + "/junctions.bed", options.junctions_output_file ) + + # Remove headers from SAM file in place. + in_header = True # Headers always at start of file. + for line in fileinput.input( tmp_output_dir + "/accepted_hits.sam", inplace=1 ): + if in_header and line.startswith("@"): + continue + else: + in_header = False + sys.stdout.write( line ) + + # Copy SAM File. + shutil.copyfile( tmp_output_dir + "/accepted_hits.sam", options.accepted_hits_output_file ) + except Exception, e: + stop_err( 'Error in tophat:\n' + str( e ) ) + finally: + # Clean up temp dirs + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + if os.path.exists( tmp_output_dir ): + shutil.rmtree( tmp_output_dir ) if __name__=="__main__": __main__() diff -r 436c9d1c5e64 -r c09a8456b63e tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml Wed Apr 28 17:35:02 2010 -0400 +++ b/tools/ngs_rna/tophat_wrapper.xml Thu Apr 29 19:57:00 2010 -0400 @@ -1,24 +1,104 @@ -<tool id="tophat" name="Tophat" version="1.0.13"> +<tool id="tophat" name="Tophat" version="1.0.0"> <description>Find splice junctions using RNA-seq data</description> <command interpreter="python"> - tophat_wrapper.py + tophat_wrapper.py + ## Change this to accomodate the number of threads you have available. --num-threads="4" - --coverage-output=$coverage - --junctions-output=$junctions + + ## Provide outputs. + --coverage-output=$coverage + --junctions-output=$junctions --hits-output=$accepted_hits + + ## Handle reference file. #if $refGenomeSource.genomeSource == "history": - --indexes-dir=$refGenomeSource.ownFile + --own-file=$refGenomeSource.ownFile + --indexes-path="None" #else: - --indexes-dir=$refGenomeSource.index.value + --own-file="None" + --indexes-path=$refGenomeSource.index.value #end if + + ## Are reads single-end or paired? + --single-paired=$singlePaired.sPaired + + ## First input file always required. + --input1=$singlePaired.input1 + + ## Set parms based on whether reads are single-end or paired. #if $singlePaired.sPaired == "single": - --input1=$singlePaired.input1 --input2="None" - #else: - -r $singlePaired.mean_inner_distance - --input1=$singlePaired.input1 - --input2=$singlePaired.input2 - #end if + -r "None" + --settings=$singlePaired.sParams.sSettingsType + #if $singlePaired.sParams.sSettingsType == "full": + --mate-std-dev="None" + -a $singlePaired.sParams.anchor_length + -m $singlePaired.sParams.splice_mismatches + -i $singlePaired.sParams.min_intron_length + -I $singlePaired.sParams.max_intron_length + -F $singlePaired.sParams.junction_filter + -g $singlePaired.sParams.max_multihits + --min-segment-intron $singlePaired.sParams.min_segment_intron + --max-segment-intron $singlePaired.sParams.max_segment_intron + --seg-mismatches=$singlePaired.sParams.seg_mismatches + --seg-length=$singlePaired.sParams.seg_length + #if $singlePaired.sParams.closure_search.use_search == "Yes": + --closure-search + --min-closure-exon $singlePaired.sParams.closure_search.min_closure_exon + --min-closure-intron $singlePaired.sParams.closure_search.min_closure_intron + --max-closure-intron $singlePaired.sParams.closure_search.max_closure_intron + #else: + --no-closure-search + #end if + #if $singlePaired.sParams.coverage_search.use_search == "Yes": + --coverage-search + --min-coverage-intron $singlePaired.sParams.coverage_search.min_coverage_intron + --max-coverage-intron $singlePaired.sParams.coverage_search.max_coverage_intron + #else: + --no-coverage-search + #end if + ## No idea why the type conversion is necessary, but it seems to be. + #if str ($singlePaired.sParams.microexon_search) == "Yes": + --microexon-search + #end if + #end if + #else: + --input2=$singlePaired.input2 + -r $singlePaired.mate_inner_distance + --settings=$singlePaired.pParams.pSettingsType + #if $singlePaired.pParams.pSettingsType == "full": + --mate-std-dev=$singlePaired.pParams.mate_std_dev + -a $singlePaired.pParams.anchor_length + -m $singlePaired.pParams.splice_mismatches + -i $singlePaired.pParams.min_intron_length + -I $singlePaired.pParams.max_intron_length + -F $singlePaired.pParams.junction_filter + -g $singlePaired.pParams.max_multihits + --min-segment-intron $singlePaired.pParams.min_segment_intron + --max-segment-intron $singlePaired.pParams.max_segment_intron + --seg-mismatches=$singlePaired.pParams.seg_mismatches + --seg-length=$singlePaired.pParams.seg_length + #if $singlePaired.pParams.closure_search.use_search == "Yes": + --closure-search + --min-closure-exon $singlePaired.pParams.closure_search.min_closure_exon + --min-closure-intron $singlePaired.pParams.closure_search.min_closure_intron + --max-closure-intron $singlePaired.pParams.closure_search.max_closure_intron + #else: + --no-closure-search + #end if + #if $singlePaired.pParams.coverage_search.use_search == "Yes": + --coverage-search + --min-coverage-intron $singlePaired.pParams.coverage_search.min_coverage_intron + --max-coverage-intron $singlePaired.pParams.coverage_search.max_coverage_intron + #else: + --no-coverage-search + #end if + ## No idea why the type conversion is necessary, but it seems to be. + #if str ($singlePaired.pParams.microexon_search) == "Yes": + --microexon-search + #end if + #end if + #end if </command> <inputs> <conditional name="refGenomeSource"> @@ -27,56 +107,219 @@ <option value="history">Use one from the history</option> </param> <when value="indexed"> - <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_file="bowtie_indices.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> - </param> - </when> + <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> + <options from_file="bowtie_indices.loc"> + <column name="value" index="1" /> + <column name="name" index="0" /> + </options> + </param> + </when> <when value="history"> <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> </when>  - </conditional>  + </conditional>  <conditional name="singlePaired"> <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> </param> <when value="single"> - <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <conditional name="sParams"> + <param name="sSettingsType" type="select" label="TopHat settings to use" help="You can use the default settings or set custom values for any of Tophat's parameters."> + <option value="preSet">Use Defaults</option> + <option value="full">Full parameter list</option> + </param> + <when value="preSet" /> +  + <when value="full"> + <param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." /> + <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" /> + <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." /> + <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /> + <param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" /> + <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /> + <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /> + <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" /> + <param name="seg_mismatches" type="integer" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /> + <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /> +  + <conditional name="closure_search"> + <param name="use_search" type="select" label="Use Closure Search"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param name="min_closure_exon" type="integer" value="50" label="During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50." /> + <param name="min_closure_intron" type="integer" value="50" label="Minimum intron length that may be found during closure search" /> + <param name="max_closure_intron" type="integer" value="5000" label="Maximum intron length that may be found during closure search" /> + </when> + <when value="No" /> + </conditional> +  + <conditional name="coverage_search"> + <param name="use_search" type="select" label="Use Coverage Search"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" /> + <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" /> + </when> + <when value="No" /> + </conditional> + <param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer."> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + </when>  + </conditional>  </when> <when value="paired"> - <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> - <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> - <param format="fastqsanger" name="mean_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs"/> + <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="mate_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs" /> + <conditional name="pParams"> + <param name="pSettingsType" type="select" label="TopHat settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> + <option value="preSet">Commonly used</option> + <option value="full">Full parameter list</option> + </param> + <when value="preSet" /> +  + <when value="full"> + <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/> + <param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." /> + <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" /> + <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." /> + <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /> + <param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" /> + <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /> + <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /> + <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" /> + <param name="seg_mismatches" type="integer" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /> + <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /> +  + <conditional name="closure_search"> + <param name="use_search" type="select" label="Use Closure Search"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param name="min_closure_exon" type="integer" value="50" label="During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50." /> + <param name="min_closure_intron" type="integer" value="50" label="Minimum intron length that may be found during closure search" /> + <param name="max_closure_intron" type="integer" value="5000" label="Maximum intron length that may be found during closure search" /> + </when> + <when value="No" /> + </conditional> +  + <conditional name="coverage_search"> + <param name="use_search" type="select" label="Use Coverage Search"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" /> + <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" /> + </when> + <when value="No" /> + </conditional> + <param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer."> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + </when>  + </conditional>  </when> </conditional> </inputs> - + <outputs> - <data format="sam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/> - <data format="wig" name="coverage" label="${tool.name} on ${on_string}: coverage"/> + <data format="sam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/> + <data format="bedgraph" name="coverage" label="${tool.name} on ${on_string}: coverage"/> <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"/> </outputs> - + <tests> +  + +  <test> - <param name="genomeSource" value="indexed"/> - <param name="index" value="test_ref"/> + <param name="genomeSource" value="history"/> + <param name="ownFile" ftype="fasta" value="tophat_in3.fa"/> <param name="sPaired" value="paired"/> <param name="input1" ftype="fastqsanger" value="tophat_in1.fq"/> <param name="input2" ftype="fastqsanger" value="tophat_in2.fq"/> - <param name="mean_inner_distance" value="20"/> -  <output name="coverage" file="tophat_out2.wig"/> <output name="junctions" file="tophat_out3.bed"/> </test> - </tests> - +  +  + </tests> + <help> **Tophat Overview** @@ -104,11 +347,15 @@ **Outputs** -Tophat produces three output files:: +Tophat produces three output files: - coverage.wig -- coverage of reads - accepted_hits.sam -- reads that were mapped onto genome - junctions.bed -- splice junctions identified by Tophat +- coverage.wig -- A UCSC BedGraph_ wigglegram track, showing the depth of coverage at each position, including the spliced read alignments. +- accepted_hits.sam -- A list of read alignments in SAM_ format. +- junctions.bed -- A UCSC BED_ track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction. + +.. _BedGraph: http://genome.ucsc.edu/goldenPath/help/bedgraph.html +.. _SAM: http://samtools.sourceforge.net/ +.. _BED: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 ------- @@ -122,8 +369,35 @@ This is a list of implemented Tophat options:: - -r This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments - selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter - is required for paired end runs. + -r This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments + selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter + is required for paired end runs. + --mate-std-dev INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp. + -a/--min-anchor-length INT The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction. Note that individual spliced + alignments may span a junction with fewer than this many bases on one side. However, every junction involved in spliced alignments is supported by at least one + read with this many bases on each side. This must be at least 3 and the default is 8. + -m/--splice-mismatches INT The maximum number of mismatches that may appear in the "anchor" region of a spliced alignment. The default is 0. + -i/--min-intron-length INT The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart. The default is 70. + -I/--max-intron-length INT The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read. The default is 500000. + -F/--min-isoform-fraction 0.0-1.0 TopHat filters out junctions supported by too few alignments. Suppose a junction spanning two exons, is supported by S reads. Let the average depth of coverage of + exon A be D, and assume that it is higher than B. If S / D is less than the minimum isoform fraction, the junction is not reported. A value of zero disables the + filter. The default is 0.15. + -g/--max-multihits INT Instructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many + alignments. The default is 40. + --no-closure-search Disables the mate pair closure-based search for junctions. Currently, has no effect - closure search is off by default. + --closure-search Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (about or less than 50bp) + --no-coverage-search Disables the coverage based search for junctions. + --coverage-search Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity. + --microexon-search With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer. + --butterfly-search TopHat will use a slower but potentially more sensitive algorithm to find junctions in addition to its standard search. Consider using this if you expect that your experiment produced a lot of reads from pre-mRNA, that fall within the introns of your transcripts. + --segment-mismatches Read segments are mapped independently, allowing up to this many mismatches in each segment alignment. The default is 2. + --segment-length Each read is cut up into segments, each at least this long. These segments are mapped independently. The default is 25. + --min-closure-exon During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50. + --min-closure-intron The minimum intron length that may be found during closure search. The default is 50. + --max-closure-intron The maximum intron length that may be found during closure search. The default is 5000. + --min-coverage-intron The minimum intron length that may be found during coverage search. The default is 50. + --max-coverage-intron The maximum intron length that may be found during coverage search. The default is 20000. + --min-segment-intron The minimum intron length that may be found during split-segment search. The default is 50. + --max-segment-intron The maximum intron length that may be found during split-segment search. The default is 500000. </help> </tool>

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[hg] galaxy 3716: trackster: BAM display supports paired-end rea...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/436c9d1c5e64 changeset: 3716:436c9d1c5e64 user: Kanwei Li <kanwei(a)gmail.com> date: Wed Apr 28 17:35:02 2010 -0400 description: trackster: BAM display supports paired-end reads, displays sequence when possible diffstat: lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py | 2 +- lib/galaxy/visualization/tracks/data/bam.py | 34 +- lib/galaxy/visualization/tracks/data/summary_tree.py | 4 +- lib/galaxy/visualization/tracks/summary.py | 6 +- lib/galaxy/web/controllers/tracks.py | 8 +- static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 284 +++++---- 7 files changed, 185 insertions(+), 155 deletions(-) diffs (524 lines): diff -r a5ccb2ba4c74 -r 436c9d1c5e64 lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py --- a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py Wed Apr 28 16:06:58 2010 -0400 +++ b/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py Wed Apr 28 17:35:02 2010 -0400 @@ -17,7 +17,7 @@ bamfile = csamtools.Samfile( filename=input_fname, mode='rb', index_filename=index_fname ) - st = SummaryTree(block_size=100, levels=4, draw_cutoff=100, detail_cutoff=20) + st = SummaryTree(block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30) for read in bamfile.fetch(): st.insert_range(bamfile.getrname(read.rname), read.pos, read.pos + read.rlen) diff -r a5ccb2ba4c74 -r 436c9d1c5e64 lib/galaxy/visualization/tracks/data/bam.py --- a/lib/galaxy/visualization/tracks/data/bam.py Wed Apr 28 16:06:58 2010 -0400 +++ b/lib/galaxy/visualization/tracks/data/bam.py Wed Apr 28 17:35:02 2010 -0400 @@ -33,12 +33,36 @@ if chrom.startswith( 'chr' ): data = bamfile.fetch( start=start, end=end, reference=chrom[3:] ) else: - raise + return None # Encode reads as list of dictionaries results = [] + paired_pending = {} for read in data: - payload = [ str(read.pos) + str(read.seq), read.pos, read.pos + read.rlen, read.seq ] - results.append(payload) + qname = read.qname + if read.is_proper_pair: + if qname in paired_pending: # one in dict is always first + pair = paired_pending[qname] + results.append( [ qname, pair['start'], read.pos + read.rlen, read.seq, [pair['start'], pair['end'], pair['seq']], [read.pos, read.pos + read.rlen, read.seq] ] ) + # results.append( [read.qname, pair['start'], read.pos + read.rlen, qname, [pair['start'], pair['end']], [read.pos, read.pos + read.rlen] ] ) + del paired_pending[qname] + else: + paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read.rlen, 'seq': read.seq, 'mate_start': read.mpos, 'rlen': read.rlen } + else: + results.append( [qname, read.pos, read.pos + read.rlen, read.seq] ) + # take care of reads whose mates are out of range + for qname, read in paired_pending.iteritems(): + if read['mate_start'] < read['start']: + start = read['mate_start'] + end = read['end'] + r1 = [read['mate_start'], read['mate_start'] + read['rlen']] + r2 = [read['start'], read['end'], read['seq']] + else: + start = read['start'] + end = read['mate_start'] + read['rlen'] + r1 = [read['start'], read['end'], read['seq']] + r2 = [read['mate_start'], read['mate_start'] + read['rlen']] + + results.append( [ qname, start, end, read['seq'], r1, r2 ] ) + bamfile.close() - return results - \ No newline at end of file + return results \ No newline at end of file diff -r a5ccb2ba4c74 -r 436c9d1c5e64 lib/galaxy/visualization/tracks/data/summary_tree.py --- a/lib/galaxy/visualization/tracks/data/summary_tree.py Wed Apr 28 16:06:58 2010 -0400 +++ b/lib/galaxy/visualization/tracks/data/summary_tree.py Wed Apr 28 17:35:02 2010 -0400 @@ -38,6 +38,6 @@ if results == "detail": return None elif results == "draw": - return "no_detail", None, None + return "no_detail" else: - return results, stats["max"], stats["avg"] + return results, stats[level]["max"], stats[level]["avg"], stats[level]["delta"] diff -r a5ccb2ba4c74 -r 436c9d1c5e64 lib/galaxy/visualization/tracks/summary.py --- a/lib/galaxy/visualization/tracks/summary.py Wed Apr 28 16:06:58 2010 -0400 +++ b/lib/galaxy/visualization/tracks/summary.py Wed Apr 28 17:35:02 2010 -0400 @@ -54,8 +54,10 @@ self.chrom_stats[chrom]["detail_level"] = level break else: - self.chrom_stats[chrom]["max"] = max_val - self.chrom_stats[chrom]["avg"] = float(max_val) / len(blocks[level]) + self.chrom_stats[chrom][level] = {} + self.chrom_stats[chrom][level]["delta"] = self.block_size ** level + self.chrom_stats[chrom][level]["max"] = max_val + self.chrom_stats[chrom][level]["avg"] = float(max_val) / len(blocks[level]) cur_best = level self.chrom_blocks[chrom] = dict([ (key, value) for key, value in blocks.iteritems() if key >= cur_best ]) diff -r a5ccb2ba4c74 -r 436c9d1c5e64 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Wed Apr 28 16:06:58 2010 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Wed Apr 28 17:35:02 2010 -0400 @@ -236,12 +236,12 @@ indexer = dataset_type_to_data_provider[data_sources['index']]( dataset.get_converted_dataset(trans, data_sources['index']), dataset ) summary = indexer.get_summary( chrom, low, high, **kwargs ) if summary is not None: - frequencies, max_v, avg_v = summary - if frequencies != "no_detail": - return { "dataset_type": data_sources['index'], "data": frequencies, "max": max_v, "avg": avg_v } - else: + if summary == "no_detail": kwargs["no_detail"] = True # meh extra_info = "no_detail" + else: + frequencies, max_v, avg_v, delta = summary + return { "dataset_type": data_sources['index'], "data": frequencies, "max": max_v, "avg": avg_v, "delta": delta } dataset_type = data_sources['data'] data_provider = dataset_type_to_data_provider[ dataset_type ]( dataset.get_converted_dataset(trans, dataset_type), dataset ) diff -r a5ccb2ba4c74 -r 436c9d1c5e64 static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Wed Apr 28 16:06:58 2010 -0400 +++ b/static/scripts/packed/trackster.js Wed Apr 28 17:35:02 2010 -0400 @@ -1,1 +1,1 @@ -var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,! "repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var Drawer=function(){};$.extend(Drawer.prototype,{intensity:function(b,a,c){},});drawer=new Drawer();var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_h! igh=0;this.center=(this.max_high-this.max_low)/2;this.zoom_factor=3;th is.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[a]},update_options:function(){var b=$("ul#sortable-ul").sortable("toArray");var d=[];var c=$("#viewport > div").sort(function(g,f){return b.indexOf($(g).attr("id"))>b.indexOf($(f).attr("id"))});$("#viewport > div").remove();$("#viewport").html(c);for(var e in view.tracks){var a=view.tracks[e];if(a.update_options){a.update_options(e)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.center=this.center=(this.max_high-this.max_low)/2;this.zoom_level=0;$(".yaxislabel").remove()},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.spa! n/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a,b){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/b.width()*(this.h! igh-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:func tion(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div></div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_N! OCONVERTER)}else{if(d.data&&d.data.length===0||d.data===null){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(k);var l=this.content_div.width()/f;var h;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-! i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append (c);this.max_height=Math.max(this.max_height,c.height())}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove! ();this.content_div.append(b)}});var LineTrack=function(c,a,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("line-track");this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_! maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.p refs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,q,c,e){if(this.vertical_range===undefined){return}var r=q*DENSITY*o,a=DENSITY*o,! b=$("<canvas class='tile'></canvas>"),u=o+"_"+q;if(this.data_cache.get(u)===undefined){this.get_data(o,q);return}var t=this.data_cache.get(u);if(t===null){return}b.css({position:"absolute",top:0,left:(r-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,s=this.total_frequency,d=this.height_px;n.beginPath();if(t.length>1){var f=Math.ceil((t[1][0]-t[0][0])*e)}else{var f=10}for(var p=0;p<t.length;p++){var j=t[p][0]-r;var h=t[p][1];if(this.prefs.mode=="Intensity"){if(h===null){continue}j=j*e;if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(j,0,f,this.height_px)}else{if(h===null){k=false;continue}else{j=j*e;if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/m*d);if(k){n.lineTo(j,h)}else{n.moveTo(j,h);k=true}}}}n.stroke();c.append(b);return b},gen_options:function(n){var a=$("<div></! div>").addClass("form-row");var h="track_"+n+"_minval",k="track_"+n+"_ maxval",e="track_"+n+"_mode",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j),d=$("<label></label>").attr("for",e).text("Display mode:"),i=(this.prefs.mode===undefined?"Line":this.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!=this.prefs.mode){this.prefs.min_value=parseFloat(a);th! is.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.! label_color=b.label_color}if(b.show_counts!==undefined){this.prefs.sho w_counts=b.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,c){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,v=[],h=0,b=$("<canvas></canvas>").get(0).getContext("2d"),n=this.view.max_low;var d,f,x=[];for(var s=0,t=g.length;s<t;s++){var e=g[s],l=e[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);x.push(this.inc_slots[a][l]! )}else{v.push(s)}}for(var s=0,t=v.length;s<t;s++){var e=g[v[s]];l=e[0],feature_start=e[1],feature_end=e[2],feature_name=e[3];d=Math.floor((feature_start-n)*m);f=Math.ceil((feature_end-n)*m);if(!c){var p=b.measureText(feature_name).width;if(d-p<0){f+=p}else{d-=p}}var r=0;while(true){var o=true;if(this.s_e_by_tile[a][r]!==undefined){for(var q=0,w=this.s_e_by_tile[a][r].length;q<w;q++){var u=this.s_e_by_tile[a][r][q];if(f>u[0]&&d<u[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][r]===undefined){this.s_e_by_tile[a][r]=[]}this.s_e_by_tile[a][r].push([d,f]);this.inc_slots[a][l]=r;h=Math.max(h,r);break}r++}}return h},draw_tile:function(R,h,m,ae){var z=h*DENSITY*R,X=(h+1)*DENSITY*R,w=DENSITY*R;var ac,ad,p;var Y=z+"_"+X;var ac=this.data_cache.get(Y);if(ac===undefined){this.data_queue[[z,X]]=true;this.get_data(z,X);return}if(ac.dataset_type=="array_tree"){p=30}else{var P=(ac.extra_info==="no_detail");var af=(P?this.vertical_nodetail_px:this.vertical_detail_px);p=this.incremental_slo! ts(this.view.zoom_res,ac.data,P)*af+15;m.parent().css("height",Math.ma x(this.height_px,p)+"px");ad=this.inc_slots[this.view.zoom_res]}var a=Math.ceil(w*ae),F=$("<canvas class='tile'></canvas>"),T=this.prefs.label_color,f=this.prefs.block_color,J=this.left_offset;F.css({position:"absolute",top:0,left:(z-this.view.low)*ae-J});F.get(0).width=a+J;F.get(0).height=p;var t=F.get(0).getContext("2d");t.fillStyle=this.prefs.block_color;t.font=this.default_font;t.textAlign="right";var C=55,W=255-C,g=W*2/3;if(ac.dataset_type=="summary_tree"){var L=ac.data;var v=ac.max;var l=ac.avg;if(ac.data.length>2){var b=Math.ceil((L[1][0]-L[0][0])*ae)}else{var b=50}for(var aa=0,s=L.length;aa<s;aa++){var N=Math.ceil((L[aa][0]-z)*ae);var M=L[aa][1];if(!M){continue}var E=Math.floor(W-(M/v)*W);t.fillStyle="rgb("+E+","+E+","+E+")";t.fillRect(N+J,0,b,20);if(this.prefs.show_counts){if(E>g){t.fillStyle="black"}else{t.fillStyle="#ddd"}t.textAlign="center";t.fillText(L[aa][1],N+J+(b/2),12)}}m.append(F);return F}var ac=ac.data;var Z=0;for(var aa=0,s=ac.length;aa<s;aa++){var G=ac! [aa],D=G[0],ab=G[1],O=G[2],A=G[3];if(ab<=X&&O>=z){var Q=Math.floor(Math.max(0,(ab-z)*ae)),u=Math.ceil(Math.min(a,(O-z)*ae)),K=ad[D]*af;if(P){t.fillRect(Q+J,K+5,u-Q,1)}else{var r=G[4],I=G[5],S=G[6],e=G[7];var q,U,B=null,ag=null;if(I&&S){B=Math.floor(Math.max(0,(I-z)*ae));ag=Math.ceil(Math.min(a,(S-z)*ae))}if(A!==undefined&&ab>z){t.fillStyle=T;if(h===0&&Q-t.measureText(A).width<0){t.textAlign="left";t.fillText(A,u+2+J,K+8)}else{t.textAlign="right";t.fillText(A,Q-2+J,K+8)}t.fillStyle=f}if(e){if(r){if(r=="+"){t.fillStyle=RIGHT_STRAND}else{if(r=="-"){t.fillStyle=LEFT_STRAND}}t.fillRect(Q+J,K,u-Q,10);t.fillStyle=f}for(var Y=0,d=e.length;Y<d;Y++){var n=e[Y],c=Math.floor(Math.max(0,(n[0]-z)*ae)),H=Math.ceil(Math.min(a,(n[1]-z)*ae));if(c>H){continue}q=5;U=3;t.fillRect(c+J,K+U,H-c,q);if(B!==undefined&&!(c>ag||H<B)){q=9;U=1;var V=Math.max(c,B),o=Math.min(H,ag);t.fillRect(V+J,K+U,o-V,q)}}}else{q=9;U=1;t.fillRect(Q+J,K+U,u-Q,q);if(G.strand){if(G.strand=="+"){t.fillStyle=RIGHT_STRAND_INV! }else{if(G.strand=="-"){t.fillStyle=LEFT_STRAND_INV}}t.fillRect(Q+J,K, u-Q,10);t.fillStyle=prefs.block_color}}}Z++}}m.append(F);return F},gen_options:function(i){var a=$("<div></div>").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label></label>").attr("for",e).text("Block color:"),l=$("<input></input>").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label></label>").attr("for",j).text("Text color:"),h=$("<input></input>").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label></label>").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div></div>").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.labe! l_color||a!=this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); \ No newline at end of file +var DEBUG=false;var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"! repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var Drawer=function(){};$.extend(Drawer.prototype,{intensity:function(b,a,c){},});drawer=new Drawer();var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_hi! gh=0;this.center=(this.max_high-this.max_low)/2;this.zoom_factor=3;thi s.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[a]},update_options:function(){var b=$("ul#sortable-ul").sortable("toArray");var d=[];var c=$("#viewport > div").sort(function(g,f){return b.indexOf($(g).attr("id"))>b.indexOf($(f).attr("id"))});$("#viewport > div").remove();$("#viewport").html(c);for(var e in view.tracks){var a=view.tracks[e];if(a.update_options){a.update_options(e)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.center=this.center=(this.max_high-this.max_low)/2;this.zoom_level=0;$(".yaxislabel").remove()},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.span! /Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a,b){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/b.width()*(this.hi! gh-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:funct ion(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div></div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NO! CONVERTER)}else{if(d.data&&d.data.length===0||d.data===null){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>"),l=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(k),this.max_height=0;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;! var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b}) ;k.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute! ",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("line-track");this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("! #track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval"). val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,q,c,e){if(this.vert! ical_range===undefined){return}var r=q*DENSITY*o,a=DENSITY*o,b=$("<canvas class='tile'></canvas>"),u=o+"_"+q;if(this.data_cache.get(u)===undefined){this.get_data(o,q);return}var t=this.data_cache.get(u);if(t===null){return}b.css({position:"absolute",top:0,left:(r-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,s=this.total_frequency,d=this.height_px;n.beginPath();if(t.length>1){var f=Math.ceil((t[1][0]-t[0][0])*e)}else{var f=10}for(var p=0;p<t.length;p++){var j=t[p][0]-r;var h=t[p][1];if(this.prefs.mode=="Intensity"){if(h===null){continue}j=j*e;if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(j,0,f,this.height_px)}else{if(h===null){k=false;continue}else{j=j*e;if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/m*d);if(k){n.lineTo(j,h)}else{n.moveTo(j,h);k=true}}}}n.stroke();c! .append(b);return b},gen_options:function(n){var a=$("<div></div>").ad dClass("form-row");var h="track_"+n+"_minval",k="track_"+n+"_maxval",e="track_"+n+"_mode",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j),d=$("<label></label>").attr("for",e).text("Display mode:"),i=(this.prefs.mode===undefined?"Line":this.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_val! ue||b!=this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(b.block_color!==undefined){this.prefs.block_! color=b.block_color}if(b.label_color!==undefined){this.prefs.label_col or=b.label_color}if(b.show_counts!==undefined){this.prefs.show_counts=b.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,c){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,v=[],h=0,b=$("<canvas></canvas>").get(0).getContext("2d"),n=this.view.max_low;var d,f,x=[];for(var s=0,t=g.length;s<t;s++){var e=g[s],l=e[0];if(this.inc_slots[a][l]!==undefined){h! =Math.max(h,this.inc_slots[a][l]);x.push(this.inc_slots[a][l])}else{v.push(s)}}for(var s=0,t=v.length;s<t;s++){var e=g[v[s]];l=e[0],feature_start=e[1],feature_end=e[2],feature_name=e[3];d=Math.floor((feature_start-n)*m);f=Math.ceil((feature_end-n)*m);if(!c){var p=b.measureText(feature_name).width;if(d-p<0){f+=p}else{d-=p}}var r=0;while(true){var o=true;if(this.s_e_by_tile[a][r]!==undefined){for(var q=0,w=this.s_e_by_tile[a][r].length;q<w;q++){var u=this.s_e_by_tile[a][r][q];if(f>u[0]&&d<u[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][r]===undefined){this.s_e_by_tile[a][r]=[]}this.s_e_by_tile[a][r].push([d,f]);this.inc_slots[a][l]=r;h=Math.max(h,r);break}r++}}return h},rect_or_text:function(n,o,g,f,m,b,d,k,e,i){n.textAlign="center";var j=Math.round(o/2);if(d!==undefined&&o>g){n.fillStyle="#555";n.fillRect(k,i+1,e,9);n.fillStyle="#eee";for(var h=0,l=d.length;h<l;h++){if(b+h>=f&&b+h<=m){var a=Math.floor(Math.max(0,(b+h-f)*o));n.fillText(d[h],a+this.left_offset+j,i+9)}}}else! {n.fillStyle="#555";n.fillRect(k,i+4,e,3)}},draw_tile:function(W,h,m,a k){var D=h*DENSITY*W,ac=(h+1)*DENSITY*W,C=DENSITY*W;var aj,r;var ad=D+"_"+ac;var w=this.data_cache.get(ad);if(w===undefined){this.data_queue[[D,ac]]=true;this.get_data(D,ac);return}if(w.dataset_type==="summary_tree"){r=30}else{var U=(w.extra_info==="no_detail");var al=(U?this.vertical_nodetail_px:this.vertical_detail_px);r=this.incremental_slots(this.view.zoom_res,w.data,U)*al+15;m.parent().css("height",Math.max(this.height_px,r)+"px");aj=this.inc_slots[this.view.zoom_res]}var a=Math.ceil(C*ak),K=$("<canvas class='tile'></canvas>"),Y=this.prefs.label_color,f=this.prefs.block_color,O=this.left_offset;K.css({position:"absolute",top:0,left:(D-this.view.low)*ak-O});K.get(0).width=a+O;K.get(0).height=r;var z=K.get(0).getContext("2d"),ah=z.measureText("A").width;z.fillStyle=this.prefs.block_color;z.font=this.default_font;z.textAlign="right";if(w.dataset_type=="summary_tree"){var J,G=55,ab=255-G,g=ab*2/3,Q=w.data,B=w.max,l=w.avg;if(Q.length>2){var b=Math.ceil((Q[1][0]-Q[0][0])*ak)}! else{var b=50}for(var af=0,v=Q.length;af<v;af++){var S=Math.ceil((Q[af][0]-D)*ak);var R=Q[af][1];if(!R){continue}J=Math.floor(ab-(R/B)*ab);z.fillStyle="rgb("+J+","+J+","+J+")";z.fillRect(S+O,0,b,20);if(this.prefs.show_counts){if(J>g){z.fillStyle="black"}else{z.fillStyle="#ddd"}z.textAlign="center";z.fillText(Q[af][1],S+O+(b/2),12)}}m.append(K);return K}var ai=w.data;var ae=0;for(var af=0,v=ai.length;af<v;af++){var L=ai[af],I=L[0],ag=L[1],T=L[2],E=L[3];if(ag<=ac&&T>=D){var V=Math.floor(Math.max(0,(ag-D)*ak)),A=Math.ceil(Math.min(a,Math.max(0,(T-D)*ak))),P=aj[I]*al;if(w.dataset_type==="bai"){z.fillStyle="#555";if(L[4] instanceof Array){var s=Math.floor(Math.max(0,(L[4][0]-D)*ak)),H=Math.ceil(Math.min(a,Math.max(0,(L[4][1]-D)*ak))),q=Math.floor(Math.max(0,(L[5][0]-D)*ak)),o=Math.ceil(Math.min(a,Math.max(0,(L[5][1]-D)*ak)));if(L[4][1]>=D&&L[4][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[4][0],L[4][2],s+O,H-s,P)}if(L[5][1]>=D&&L[5][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[5][0],L[5! ][2],q+O,o-q,P)}if(q>H){z.fillStyle="#999";z.fillRect(H+O,P+5,q-H,1)}} else{z.fillStyle="#555";this.rect_or_text(z,ak,ah,D,ac,ag,E,V+O,A-V,P)}if(!U&&ag>D){z.fillStyle=this.prefs.label_color;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(I,A+2+O,P+8)}else{z.textAlign="right";z.fillText(I,V-2+O,P+8)}z.fillStyle="#555"}}else{if(w.dataset_type==="interval_index"){if(U){z.fillRect(V+O,P+5,A-V,1)}else{var u=L[4],N=L[5],X=L[6],e=L[7];var t,Z,F=null,am=null;if(N&&X){F=Math.floor(Math.max(0,(N-D)*ak));am=Math.ceil(Math.min(a,Math.max(0,(X-D)*ak)))}if(E!==undefined&&ag>D){z.fillStyle=Y;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(E,A+2+O,P+8)}else{z.textAlign="right";z.fillText(E,V-2+O,P+8)}z.fillStyle=f}if(e){if(u){if(u=="+"){z.fillStyle=RIGHT_STRAND}else{if(u=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(V+O,P,A-V,10);z.fillStyle=f}for(var ad=0,d=e.length;ad<d;ad++){var n=e[ad],c=Math.floor(Math.max(0,(n[0]-D)*ak)),M=Math.ceil(Math.min(a,Math.max((n[1]-D)*ak)));if(c>M){continue}t=5;Z=3;z.fillRect(c+O,P+Z,M-c,t);i! f(F!==undefined&&!(c>am||M<F)){t=9;Z=1;var aa=Math.max(c,F),p=Math.min(M,am);z.fillRect(aa+O,P+Z,p-aa,t)}}}else{t=9;Z=1;z.fillRect(V+O,P+Z,A-V,t);if(L.strand){if(L.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(L.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(V+O,P,A-V,10);z.fillStyle=prefs.block_color}}}}}ae++}}m.append(K);return K},gen_options:function(i){var a=$("<div></div>").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label></label>").attr("for",e).text("Block color:"),l=$("<input></input>").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label></label>").attr("for",j).text("Text color:"),h=$("<input></input>").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label></label>").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div></div>").appen! d(b).append(c);return a.append(k).append(l).append(g).append(h).append (d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!=this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); \ No newline at end of file diff -r a5ccb2ba4c74 -r 436c9d1c5e64 static/scripts/trackster.js --- a/static/scripts/trackster.js Wed Apr 28 16:06:58 2010 -0400 +++ b/static/scripts/trackster.js Wed Apr 28 17:35:02 2010 -0400 @@ -3,7 +3,7 @@ */ var DEBUG = false; -var DENSITY = 1000, +var DENSITY = 200, FEATURE_LEVELS = 10, DATA_ERROR = "There was an error in indexing this dataset.", DATA_NOCONVERTER = "A converter for this dataset is not installed. Please check your datatypes_conf.xml file.", @@ -271,16 +271,15 @@ range = high - low, resolution = this.view.resolution; - if (DEBUG) { $("#debug").text(resolution + " " + this.view.zoom_res); } - var parent_element = $("<div style='position: relative;'></div>"); - this.content_div.children( ":first" ).remove(); - this.content_div.append( parent_element ); + var parent_element = $("<div style='position: relative;'></div>"), + w_scale = this.content_div.width() / range, + tile_element; - var w_scale = this.content_div.width() / range; - - var tile_element; + this.content_div.children( ":first" ).remove(); + this.content_div.append( parent_element ), + this.max_height = 0; // Index of first tile that overlaps visible region var tile_index = Math.floor( low / resolution / DENSITY ); while ( ( tile_index * DENSITY * resolution ) < high ) { @@ -298,6 +297,7 @@ // Our responsibility to move the element to the new parent parent_element.append( cached ); this.max_height = Math.max( this.max_height, cached.height() ); + this.content_div.css("height", this.max_height + "px"); } else { this.delayed_draw(this, key, low, high, tile_index, resolution, parent_element, w_scale); } @@ -311,7 +311,7 @@ if ( tile_element ) { track.tile_cache.set(key, tile_element); track.max_height = Math.max( track.max_height, tile_element.height() ); - track.content_div.css( "height", track.max_height + "px"); + track.content_div.css("height", track.max_height + "px"); } } }, 50); @@ -679,12 +679,30 @@ return highest_slot; }, + rect_or_text: function( ctx, w_scale, px_per_char, tile_low, tile_high, feature_start, name, x, x_len, y_center ) { + ctx.textAlign = "center"; + var gap = Math.round(w_scale / 2); + if (name !== undefined && w_scale > px_per_char) { + ctx.fillStyle = "#555"; + ctx.fillRect(x, y_center + 1, x_len, 9); + ctx.fillStyle = "#eee"; + for (var c = 0, str_len = name.length; c < str_len; c++) { + if (feature_start + c >= tile_low && feature_start + c <= tile_high) { + var c_start = Math.floor( Math.max(0, (feature_start + c - tile_low) * w_scale) ); + ctx.fillText(name[c], c_start + this.left_offset + gap, y_center + 9); + } + } + } else { + ctx.fillStyle = "#555"; + ctx.fillRect(x, y_center + 4, x_len, 3); + } + }, draw_tile: function( resolution, tile_index, parent_element, w_scale ) { var tile_low = tile_index * DENSITY * resolution, tile_high = ( tile_index + 1 ) * DENSITY * resolution, tile_span = DENSITY * resolution; // console.log("drawing " + tile_index); - var data, slots, required_height; + var slots, required_height; /*for (var k in this.data_cache.obj_cache) { var k_split = k.split("_"), k_low = k_split[0], k_high = k_split[1]; @@ -696,23 +714,22 @@ // var k = this.view.low + '_' + this.view.high; var k = tile_low + '_' + tile_high; - var data = this.data_cache.get(k); + var result = this.data_cache.get(k); - if (data === undefined) { + if (result === undefined) { this.data_queue[ [tile_low, tile_high] ] = true; this.get_data(tile_low, tile_high); return; } - if (data.dataset_type == "array_tree") { + if (result.dataset_type === "summary_tree") { required_height = 30; - // Blah } else { // Calculate new slots incrementally for this new chunk of data and update height if necessary - var no_detail = (data.extra_info === "no_detail"); + var no_detail = (result.extra_info === "no_detail"); var y_scale = ( no_detail ? this.vertical_nodetail_px : this.vertical_detail_px ); - required_height = this.incremental_slots( this.view.zoom_res, data.data, no_detail ) * y_scale + 15; + required_height = this.incremental_slots( this.view.zoom_res, result.data, no_detail ) * y_scale + 15; parent_element.parent().css("height", Math.max(this.height_px, required_height) + "px"); slots = this.inc_slots[this.view.zoom_res]; } @@ -732,20 +749,21 @@ new_canvas.get(0).width = width + left_offset; new_canvas.get(0).height = required_height; // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); - var ctx = new_canvas.get(0).getContext("2d"); + var ctx = new_canvas.get(0).getContext("2d"), + px_per_char = ctx.measureText("A").width; ctx.fillStyle = this.prefs.block_color; ctx.font = this.default_font; ctx.textAlign = "right"; - var min_color = 55, - color_span = 255 - min_color, - color_cutoff = color_span*2/3; // Where text switches from black to white - - if (data.dataset_type == "summary_tree") { - var points = data.data; - var max = data.max; - var avg = data.avg; - if (data.data.length > 2) { + if (result.dataset_type == "summary_tree") { + var color, + min_color = 55, + color_span = 255 - min_color, + color_cutoff = color_span*2/3, // Where text switches from black to white + points = result.data, + max = result.max, + avg = result.avg; + if (points.length > 2) { var delta_x_px = Math.ceil((points[1][0] - points[0][0]) * w_scale); } else { var delta_x_px = 50; // Arbitrary, fix @@ -756,7 +774,7 @@ var y = points[i][1]; if (!y) { continue; } - var color = Math.floor( color_span - (y / max) * color_span ); + color = Math.floor( color_span - (y / max) * color_span ); ctx.fillStyle = "rgb(" +color+ "," +color+ "," +color+ ")"; ctx.fillRect(x + left_offset, 0, delta_x_px, 20); @@ -770,11 +788,12 @@ ctx.fillText(points[i][1], x + left_offset + (delta_x_px/2), 12); } } + parent_element.append( new_canvas ); return new_canvas; } - var data = data.data; + var data = result.data; var j = 0; for (var i = 0, len = data.length; i < len; i++) { var feature = data[i], @@ -785,80 +804,118 @@ if (feature_start <= tile_high && feature_end >= tile_low) { var f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), - f_end = Math.ceil( Math.min(width, (feature_end - tile_low) * w_scale) ), + f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), y_center = slots[feature_uid] * y_scale; - - // console.log(feature_uid, feature_start, feature_end, f_start, f_end, y_center); - if (no_detail) { - ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, 1); - } else { - // Showing labels, blocks, details - var feature_strand = feature[4], - feature_ts = feature[5], - feature_te = feature[6], - feature_blocks = feature[7]; - var thickness, y_start, thick_start = null, thick_end = null; - if (feature_ts && feature_te) { - thick_start = Math.floor( Math.max(0, (feature_ts - tile_low) * w_scale) ); - thick_end = Math.ceil( Math.min(width, (feature_te - tile_low) * w_scale) ); + if (result.dataset_type === "bai") { + ctx.fillStyle = "#555"; + if (feature[4] instanceof Array) { + var b1_start = Math.floor( Math.max(0, (feature[4][0] - tile_low) * w_scale) ), + b1_end = Math.ceil( Math.min(width, Math.max(0, (feature[4][1] - tile_low) * w_scale)) ), + b2_start = Math.floor( Math.max(0, (feature[5][0] - tile_low) * w_scale) ), + b2_end = Math.ceil( Math.min(width, Math.max(0, (feature[5][1] - tile_low) * w_scale)) ); + + if (feature[4][1] >= tile_low && feature[4][0] <= tile_high) { + this.rect_or_text(ctx, w_scale, px_per_char, tile_low, tile_high, feature[4][0], feature[4][2], b1_start + left_offset, b1_end - b1_start, y_center); + } + if (feature[5][1] >= tile_low && feature[5][0] <= tile_high) { + this.rect_or_text(ctx, w_scale, px_per_char, tile_low, tile_high, feature[5][0], feature[5][2], b2_start + left_offset, b2_end - b2_start, y_center); + } + if (b2_start > b1_end) { + ctx.fillStyle = "#999"; + ctx.fillRect(b1_end + left_offset, y_center + 5, b2_start - b1_end, 1); + } + } else { + ctx.fillStyle = "#555"; + this.rect_or_text(ctx, w_scale, px_per_char, tile_low, tile_high, feature_start, feature_name, f_start + left_offset, f_end - f_start, y_center); } - if (feature_name !== undefined && feature_start > tile_low) { - ctx.fillStyle = label_color; + if (!no_detail && feature_start > tile_low) { + // Draw label + ctx.fillStyle = this.prefs.label_color; if (tile_index === 0 && f_start - ctx.measureText(feature_name).width < 0) { ctx.textAlign = "left"; - ctx.fillText(feature_name, f_end + 2 + left_offset, y_center + 8); + ctx.fillText(feature_uid, f_end + 2 + left_offset, y_center + 8); } else { ctx.textAlign = "right"; - ctx.fillText(feature_name, f_start - 2 + left_offset, y_center + 8); + ctx.fillText(feature_uid, f_start - 2 + left_offset, y_center + 8); } - ctx.fillStyle = block_color; + ctx.fillStyle = "#555"; } - if (feature_blocks) { - // Draw introns - if (feature_strand) { - if (feature_strand == "+") { - ctx.fillStyle = RIGHT_STRAND; - } else if (feature_strand == "-") { - ctx.fillStyle = LEFT_STRAND; + + } else if (result.dataset_type === "interval_index") { + + // console.log(feature_uid, feature_start, feature_end, f_start, f_end, y_center); + if (no_detail) { + ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, 1); + } else { + // Showing labels, blocks, details + var feature_strand = feature[4], + feature_ts = feature[5], + feature_te = feature[6], + feature_blocks = feature[7]; + + var thickness, y_start, thick_start = null, thick_end = null; + if (feature_ts && feature_te) { + thick_start = Math.floor( Math.max(0, (feature_ts - tile_low) * w_scale) ); + thick_end = Math.ceil( Math.min(width, Math.max(0, (feature_te - tile_low) * w_scale)) ); + } + if (feature_name !== undefined && feature_start > tile_low) { + ctx.fillStyle = label_color; + if (tile_index === 0 && f_start - ctx.measureText(feature_name).width < 0) { + ctx.textAlign = "left"; + ctx.fillText(feature_name, f_end + 2 + left_offset, y_center + 8); + } else { + ctx.textAlign = "right"; + ctx.fillText(feature_name, f_start - 2 + left_offset, y_center + 8); } - ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, 10); ctx.fillStyle = block_color; } + if (feature_blocks) { + // Draw introns + if (feature_strand) { + if (feature_strand == "+") { + ctx.fillStyle = RIGHT_STRAND; + } else if (feature_strand == "-") { + ctx.fillStyle = LEFT_STRAND; + } + ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, 10); + ctx.fillStyle = block_color; + } - for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) { - var block = feature_blocks[k], - block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), - block_end = Math.ceil( Math.min(width, (block[1] - tile_low) * w_scale) ); - if (block_start > block_end) { continue; } - // Draw the block - thickness = 5; - y_start = 3; - ctx.fillRect(block_start + left_offset, y_center + y_start, block_end - block_start, thickness); + for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) { + var block = feature_blocks[k], + block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), + block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) ); + if (block_start > block_end) { continue; } + // Draw the block + thickness = 5; + y_start = 3; + ctx.fillRect(block_start + left_offset, y_center + y_start, block_end - block_start, thickness); - // Draw thick regions: check if block intersects with thick region - if (thick_start !== undefined && !(block_start > thick_end || block_end < thick_start) ) { - thickness = 9; - y_start = 1; - var block_thick_start = Math.max(block_start, thick_start), - block_thick_end = Math.min(block_end, thick_end); - ctx.fillRect(block_thick_start + left_offset, y_center + y_start, block_thick_end - block_thick_start, thickness); + // Draw thick regions: check if block intersects with thick region + if (thick_start !== undefined && !(block_start > thick_end || block_end < thick_start) ) { + thickness = 9; + y_start = 1; + var block_thick_start = Math.max(block_start, thick_start), + block_thick_end = Math.min(block_end, thick_end); + ctx.fillRect(block_thick_start + left_offset, y_center + y_start, block_thick_end - block_thick_start, thickness); + } } - } - } else { - // If there are no blocks, we treat the feature as one big exon - thickness = 9; - y_start = 1; - ctx.fillRect(f_start + left_offset, y_center + y_start, f_end - f_start, thickness); - if ( feature.strand ) { - if (feature.strand == "+") { - ctx.fillStyle = RIGHT_STRAND_INV; - } else if (feature.strand == "-") { - ctx.fillStyle = LEFT_STRAND_INV; + } else { + // If there are no blocks, we treat the feature as one big exon + thickness = 9; + y_start = 1; + ctx.fillRect(f_start + left_offset, y_center + y_start, f_end - f_start, thickness); + if ( feature.strand ) { + if (feature.strand == "+") { + ctx.fillStyle = RIGHT_STRAND_INV; + } else if (feature.strand == "-") { + ctx.fillStyle = LEFT_STRAND_INV; + } + ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, 10); + ctx.fillStyle = prefs.block_color; } - ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, 10); - ctx.fillStyle = prefs.block_color; } } } @@ -899,62 +956,9 @@ var ReadTrack = function ( name, dataset_id, prefs ) { FeatureTrack.call( this, name, dataset_id, prefs ); this.track_type = "ReadTrack"; + this.vertical_detail_px = 10; + this.vertical_nodetail_px = 5; }; $.extend( ReadTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, { - /*draw_tile: function( resolution, tile_index, parent_element, w_scale ) { - if (!this.values) { - return; - } - var tile_low = tile_index * DENSITY * resolution, - tile_high = ( tile_index + 1 ) * DENSITY * resolution, - tile_span = DENSITY * resolution; - // console.log("drawing " + tile_index); - // Once we zoom in enough, show name labels - var data, slots, required_height; - required_height = this.height_px; - slots = this.zo_slots; - data = this.values; - - // console.log(tile_low, tile_high, tile_length, w_scale); - var width = Math.ceil( tile_span * w_scale ), - new_canvas = $("<canvas class='tile'></canvas>"); - - new_canvas.css({ - position: "absolute", - top: 0, - left: ( tile_low - this.view.low ) * w_scale - this.left_offset - }); - new_canvas.get(0).width = width + this.left_offset; - new_canvas.get(0).height = required_height; - // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); - var ctx = new_canvas.get(0).getContext("2d"); - ctx.fillStyle = this.prefs.block_color; - ctx.font = this.default_font; - ctx.textAlign = "right"; - var px_per_char = ctx.measureText("A").width; - - var j = 0; - for (var i = 0, len = data.length; i < len; i++) { - var feature = data[i]; - if (feature.start <= tile_high && feature.end >= tile_low) { - var f_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ), - f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), - y_center = slots[feature.uid] * this.vertical_detail_px; - - var thickness, y_start, thick_start = null, thick_end = null; - if (w_scale > px_per_char) { - for (var c = 0, str_len = feature.name.length; c < str_len; c++) { - var c_start = Math.floor( Math.max(0, (feature.start + c - tile_low) * w_scale) ); - ctx.fillText(feature.name[c], c_start + this.left_offset, y_center + 8); - } - } else { - ctx.fillRect(f_start + this.left_offset, y_center + 4, f_end - f_start, 3); - } - } - } - - parent_element.append( new_canvas ); - return new_canvas; - }*/ });

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[hg] galaxy 3715: Another rev on cuffcompare wrapper.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/a5ccb2ba4c74 changeset: 3715:a5ccb2ba4c74 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Wed Apr 28 16:06:58 2010 -0400 description: Another rev on cuffcompare wrapper. diffstat: tools/ngs_rna/cuffcompare_wrapper.py | 16 +++++++++++----- tools/ngs_rna/cuffcompare_wrapper.xml | 24 +++++++++++++++++++----- 2 files changed, 30 insertions(+), 10 deletions(-) diffs (83 lines): diff -r b70d9444f29f -r a5ccb2ba4c74 tools/ngs_rna/cuffcompare_wrapper.py --- a/tools/ngs_rna/cuffcompare_wrapper.py Wed Apr 28 14:54:55 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.py Wed Apr 28 16:06:58 2010 -0400 @@ -13,6 +13,8 @@ parser.add_option( '-R', action="store_true", dest='ignore_nonoverlap', help='If -r was specified, this option causes cuffcompare to ignore reference transcripts that are not overlapped by any transcript in one of cuff1.gtf,...,cuffN.gtf. Useful for ignoring annotated transcripts that are not present in your RNA-Seq samples and thus adjusting the "sensitivity" calculation in the accuracy report written in the transcripts accuracy file' ) # Wrapper / Galaxy options. + parser.add_option( '-1', dest='input1') + parser.add_option( '-2', dest='input2') parser.add_option( '-A', '--transcripts-accuracy-output', dest='transcripts_accuracy_output_file', help='' ) parser.add_option( '-B', '--transcripts-combined-output', dest='transcripts_combined_output_file', help='' ) parser.add_option( '-C', '--transcripts-tracking-output', dest='transcripts_tracking_output_file', help='' ) @@ -37,9 +39,10 @@ print cmd # Add input files. - if type(args) is list: - args = " ".join(args) - cmd += " " + args + cmd += " %s" % options.input1 + two_inputs = ( options.input2 != None) + if two_inputs: + cmd += " %s" % options.input2 # Run command. try: @@ -76,8 +79,11 @@ try: try: shutil.copyfile( tmp_output_dir + "/cc_output", options.transcripts_accuracy_output_file ) - shutil.copyfile( tmp_output_dir + "/cc_output.combined.gtf", options.transcripts_combined_output_file ) - shutil.copyfile( tmp_output_dir + "/cc_output.tracking", options.transcripts_tracking_output_file ) + if two_inputs: + shutil.copyfile( tmp_output_dir + "/cc_output.combined.gtf", options.transcripts_combined_output_file ) + shutil.copyfile( tmp_output_dir + "/cc_output.tracking", options.transcripts_tracking_output_file ) + + # TODO: also copy *.tmap, *.refmap to outputs? except Exception, e: stop_err( 'Error in cuffcompare:\n' + str( e ) ) finally: diff -r b70d9444f29f -r a5ccb2ba4c74 tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml Wed Apr 28 14:54:55 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Wed Apr 28 16:06:58 2010 -0400 @@ -3,20 +3,34 @@ <command interpreter="python"> cuffcompare_wrapper.py --transcripts-accuracy-output=$transcripts_accuracy - --transcripts-combined-output=$transcripts_combined - --transcripts-tracking-output=$transcripts_tracking + #if $second_gtf.use_second_gtf == "Yes": + --transcripts-combined-output=$transcripts_combined + --transcripts-tracking-output=$transcripts_tracking + #end if #if $annotation.use_ref_annotation == "Yes": -r $annotation.reference_annotation #if $annotation.ignore_nonoverlapping_reference: -R #end if #end if - $input1 - $input2 + -1 $input1 + #if $second_gtf.use_second_gtf == "Yes": + -2 $second_gtf.input2 + #end if </command> <inputs> <param format="gtf" name="input1" type="data" label="GTF file produced by Cufflinks" help=""/> - <param format="gtf" name="input2" type="data" label="GTF file produced by Cufflinks" help=""/> + <conditional name="second_gtf"> + <param name="use_second_gtf" type="select" label="Use Another GTF file producted by Cufflinks?"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param format="gtf" name="input2" type="data" label="GTF file produced by Cufflinks" help=""/> + </when> + <when value="No"> + </when> + </conditional> <conditional name="annotation"> <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> <option value="No">No</option>

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