September 2010 - galaxy-commits - lists.galaxyproject.org

galaxy-dist commit ff9b7abb6b60: Merge.
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannonbaker(a)me.com> # Date 1283270353 14400 # Node ID ff9b7abb6b60850b014496b8756fef1f4440c0d7 # Parent b19a56845706a85e5124bd2dd26788752db9c8ef # Parent 65edd8e2a3a8872252d9008ad2fe9dee7cbd5856 Merge.

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galaxy-dist commit 568f8d3854e8: lims: adding a file missed in the previous commit
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1283286628 14400 # Node ID 568f8d3854e8fcae7f78fbe906971a2369c65c33 # Parent d9276a4a775a7582a51cedab7b7b2b315109c53f lims: adding a file missed in the previous commit --- /dev/null +++ b/templates/requests/common/find.mako @@ -0,0 +1,101 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +<script type="text/javascript"> +$( function() { + $( "select[refresh_on_change='true']").change( function() { + var refresh = false; + var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) + if ( refresh_on_change_values ) { + refresh_on_change_values = refresh_on_change_values.value.split( ',' ); + var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); + for( i= 0; i < refresh_on_change_values.length; i++ ) { + if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ + refresh = true; + break; + } + } + } + else { + refresh = true; + } + if ( refresh ){ + $( "#find_request" ).submit(); + } + }); +}); +</script> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js("jquery.autocomplete", "autocomplete_tagging" )} +</%def> + +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "autocomplete_tagging" )} +</%def> + +<br/> +<br/> +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller=cntrller, cntrller=cntrller, action='list')}"> + <span>Browse requests</span></a> + </li> +</ul> + +<div class="toolForm"> + <div class="toolFormTitle">Find samples</div> + <div class="toolFormBody"> + <form name="find_request" id="find_request" action="${h.url_for( controller='requests_common', action='find', cntrller=cntrller)}" method="post" > + <div class="form-row"> + <label>Find in sequencing requests in state:</label> + <select name="select_search_type"> + <option value="In-Progress" selected>In-Progress</option> + <option value="Complete">Complete</option> + <option value="Both">Both</option> + </select> + </div> + <div class="form-row"> + <label>Find by sample:</label> + <select name="search_type"> + <option value="name" selected>name</option> + <option value="bar_code">barcode</option> + </select> + </div> + <div class="form-row"> + <input type="text" name="search_string" size="40" value=""> + <input type="submit" name="go_button" value="Go"/> + </div> + %if results: + <div class="form-row"> + <label><i>${results}</i></label> + </div> + %endif + <div class="form-row"> + %if samples: + %for s in samples: + <div class="form-row"> + <a href="${h.url_for( controller=cntrller, action='list', operation='show', id=trans.security.encode_id(s.request.id))}"><label>Sequencing request: ${s.request.name} | Type: ${s.request.type.name} | State: ${s.request.state()}</label></a> + %if cntrller == 'requests_admin': + <i>User: ${s.request.user.email}</i> + %endif + <div class="toolParamHelp" style="clear: both;"> + Sample: ${s.name}<br/> + Barcode: ${s.bar_code}<br/> + State: ${s.current_state().name} + </div> + </div> + <br/> + %endfor + %endif + + </div> + </form> + </div> +</div>

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galaxy-dist commit 03d06d05bf62: Slight makeover to Galaxy tabs: (a) added published item links to 'Data Libraries' tab; (b) standardized personal item lists as 'Saved XXXs'; and (c) added defaults action for Visualization tab. Also extended tab generator function to handle the generation of all menu items and types.
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1283291669 14400 # Node ID 03d06d05bf62a6444f1a652910708fde17fa189b # Parent c472ac58348b0cd6d7e2040e4c5b2bfb4f42724e Slight makeover to Galaxy tabs: (a) added published item links to 'Data Libraries' tab; (b) standardized personal item lists as 'Saved XXXs'; and (c) added defaults action for Visualization tab. Also extended tab generator function to handle the generation of all menu items and types. --- a/templates/workflow/list_published.mako +++ b/templates/workflow/list_published.mako @@ -4,7 +4,7 @@ <% self.has_left_panel=False self.has_right_panel=False - self.active_view="page" + self.active_view="" self.message_box_visible=False %></%def> @@ -24,8 +24,6 @@ <%def name="center_panel()"> - ## <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="page", action="list" )}"></iframe> - <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> ${h.to_unicode( grid )} --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -12,7 +12,10 @@ <table class="tab-group" border="0" cellspacing="0" style="margin: auto;"><tr> - <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='' )"> + <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='', menu_options=None )"> + ## Create a tab at the top of the panels. menu_options is a list of 2-elements lists of [name, link] + ## that are options in the menu. + <% cls = "tab" if extra_class: @@ -23,120 +26,127 @@ if not visible: style = "display: none;" %> - <td class="${cls}" style="${style}"><a target="${target}" href="${href}">${display}</a></td> + <td class="${cls}" style="${style}"><a target="${target}" href="${href}">${display}</a> + %if menu_options: + <div class="submenu"> + <ul> + %for menu_item in menu_options: + <li> + %if not menu_item: + <hr style="color: inherit; background-color: gray"/></li> + %else: + %if len ( menu_item ) == 1: + ${menu_item[0]} + %elif len ( menu_item ) == 2: + <% name, link = menu_item %> + <a href="${link}">${name}</a></li> + %else: + <% name, link, target = menu_item %> + <a target="${target}" href="${link}">${name}</a></li> + %endif + %endif + %endfor + </ul> + </div> + %endif + </td></%def> - %if app.config.cloud_controller_instance: - ${tab( "cloud", "Cloud", h.url_for( controller='/cloud', action='index' ))} - %else: - ${tab( "analysis", "Analyze Data", h.url_for( controller='/root', action='index' ))} - - ${tab( "workflow", "Workflow", h.url_for( controller='/workflow', action='index' ))} - - ${tab( "libraries", "Data Libraries", h.url_for( controller='/library', action='index' ))} - %endif + + ## Analyze data tab. + ${tab( "analysis", "Analyze Data", h.url_for( controller='/root', action='index' ) )} + ## Workflow tab. + ${tab( "workflow", "Workflow", h.url_for( controller='/workflow', action='index' ) )} + + ## 'Shared Items' or Libraries tab. + <% + menu_options = [ + [ 'Data Libraries', h.url_for( controller='/library', action='index') ], + None, + [ 'Published Histories', h.url_for( controller='/history', action='list_published' ) ], + [ 'Published Workflows', h.url_for( controller='/workflow', action='list_published' ) ], + [ 'Published Visualizations', h.url_for( controller='/visualization', action='list_published' ) ], + [ 'Published Pages', h.url_for( controller='/page', action='list_published' ) ] + ] + tab( "libraries", "Data Libraries", h.url_for( controller='/library', action='index'), menu_options=menu_options ) + %> + + ## Lab menu. %if trans.user and trans.user.accessible_request_types(trans): - <td class="tab"> - <a>Lab</a> - <div class="submenu"> - <ul> - <li><a href="${h.url_for( controller='/requests', action='index' )}">Sequencing requests</a></li> - <li><a href="${h.url_for( controller='/requests_common', action='find', cntrller='requests' )}">Find samples</a></li> - <li><a target="_blank" href="${app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" )}">Help</a></li> - </ul> - </div> - </td> + menu_options = [ + [ 'Sequencing Requests', h.url_for( controller='/requests', action='index' ) ], + [ 'Find Samples', h.url_for( controller='/requests_common', action='find' ) ], + [ 'Help', app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" )}, "galaxy_main" ], + ] + tab( "lab", "Lab", None, menu_options=menu_options ) %endif + ## Visualization menu. %if app.config.get_bool( 'enable_tracks', False ): - <% - cls = "tab" - if self.active_view == 'visualization': - cls += " active" - %> - <td class="${cls}"> - Visualization - <div class="submenu"> - <ul> - <li><a href="${h.url_for( controller='/tracks', action='index' )}">New Track Browser</a></li> - <li><hr style="color: inherit; background-color: gray"/></li> - <li><a href="${h.url_for( controller='/visualization', action='list' )}">Saved Visualizations</a></li> - </ul> - </div> - </td> + <% + menu_options = [ + ['New Track Browser', h.url_for( controller='/tracks', action='index' ) ], + ['Saved Visualizations', h.url_for( controller='/visualization', action='list' ) ] + ] + tab( "visualization", "Visualization", h.url_for( controller='/visualization', action='list'), menu_options=menu_options ) + %> %endif + ## Admin tab. ${tab( "admin", "Admin", h.url_for( controller='/admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} - <td class="tab"> - <a>Help</a> - <div class="submenu"> - <ul> - <li><a href="${app.config.get( "bugs_email", "mailto:galaxy-bugs@bx.psu.edu" )}">Email comments, bug reports, or suggestions</a></li> - <li><a target="_blank" href="${app.config.get( "wiki_url", "http://bitbucket.org/galaxy/galaxy-central/wiki" )}">Galaxy Wiki</a></li> - <li><a target="_blank" href="${app.config.get( "screencasts_url", "http://galaxycast.org" )}">Video tutorials (screencasts)</a></li> - <li><a target="_blank" href="${app.config.get( "citation_url", "http://bitbucket.org/galaxy/galaxy-central/wiki/Citations" )}">How to Cite Galaxy</a></li> - </ul> - </div> - </td> + ## Help tab. + <% + menu_options = [ + ['Email comments, bug reports, or suggestions', app.config.get( "bugs_email", "mailto:galaxy-bugs@bx.psu.edu" ) ], + ['Galaxy Wiki', app.config.get( "wiki_url", "http://bitbucket.org/galaxy/galaxy-central/wiki" ), "_blank" ], + ['Video tutorials (screencasts)', app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], + ['How to Cite Galaxy', app.config.get( "screencasts_url", "http://bitbucket.org/galaxy/galaxy-central/wiki/Citations" ), "_blank" ] + ] + tab( "help", "Help", None, menu_options=menu_options) + %> - ## User tab. - <% - cls = "tab" - if self.active_view == 'user': - cls += " active" + ## User tabs. + <% + # Menu for user who is not logged in. + menu_options = [ [ "Login", h.url_for( controller='/user', action='login' ), "galaxy_main" ] ] + if app.config.allow_user_creation: + menu_options.append( [ "Register", h.url_for( controller='/user', action='create' ), "galaxy_main" ] ) + extra_class = "loggedout-only" + visible = ( trans.user == None ) + tab( "user", "User", None, visible=visible, menu_options=menu_options ) + + # Menu for user who is logged in. + if trans.user: + email = trans.user.email + else: + email = "" + menu_options = [ [ '<li>Logged in as <span id="user-email">%s</span></li>' % email ] ] + if app.config.use_remote_user: + if app.config.remote_user_logout_href: + menu_options.append( [ 'Logout', app.config.remote_user_logout_href, "galaxy_main" ] ) + else: + menu_options.append( [ 'Preferences', h.url_for( controller='/user', action='index' ), "galaxy_main" ] ) + if app.config.get_bool( 'enable_tracks', False ): + menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] ) + if app.config.require_login: + logout_url = h.url_for( controller='/root', action='index', m_c='user', m_a='logout' ) + else: + logout_url = h.url_for( controller='/user', action='logout' ) + menu_options.append( [ 'Logout', logout_url, "_top" ] ) + menu_options.append( None ) + menu_options.append( [ 'Saved Histories', h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) + menu_options.append( [ 'Saved Datasets', h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) + if app.config.get_bool( 'enable_pages', False ): + menu_options.append( [ 'Saved Pages', h.url_for( controller='/page', action='list' ), "_top" ] ) + if app.config.enable_api: + menu_options.append( [ 'API Keys', h.url_for( controller='/user', action='api_keys' ), "galaxy_main" ] ) + + extra_class = "loggedin-only" + visible = ( trans.user != None ) + tab( "user", "User", None, visible=visible, menu_options=menu_options ) %> - <td class="${cls}"> - <a>User</a> - <% - if trans.user: - user_email = trans.user.email - style1 = "display: none;" - style2 = ""; - else: - user_email = "" - style1 = "" - style2 = "display: none;" - %> - <div class="submenu"> - <ul class="loggedout-only" style="${style1}"> - <li><a target="galaxy_main" href="${h.url_for( controller='/user', action='login' )}">Login</a></li> - %if app.config.allow_user_creation: - <li><a target="galaxy_main" href="${h.url_for( controller='/user', action='create' )}">Register</a></li> - %endif - </ul> - <ul class="loggedin-only" style="${style2}"> - <li>Logged in as <span id="user-email">${user_email}</span></li> - %if app.config.use_remote_user: - %if app.config.remote_user_logout_href: - <li><a target="galaxy_main" href="${app.config.remote_user_logout_href}">Logout</a></li> - %endif - %else: - <li><a target="galaxy_main" href="${h.url_for( controller='/user', action='index' )}">Preferences</a></li> - <% - if app.config.require_login: - logout_url = h.url_for( controller='/root', action='index', m_c='user', m_a='logout' ) - else: - logout_url = h.url_for( controller='/user', action='logout' ) - %> - %if app.config.get_bool( 'enable_tracks', False ): - <li><a target="galaxy_main" href="${h.url_for( controller='/user', action='dbkeys' )}">Custom Builds</a></li> - %endif - <li><a target="_top" href="${logout_url}">Logout</a></li> - <li><hr style="color: inherit; background-color: gray"/></li> - %endif - <li><a target="galaxy_main" href="${h.url_for( controller='/history', action='list' )}">Histories</a></li> - <li><a target="galaxy_main" href="${h.url_for( controller='/dataset', action='list' )}">Datasets</a></li> - %if app.config.get_bool( 'enable_pages', False ): - <li><a href="${h.url_for( controller='/page', action='list' )}">Pages</a></li> - %endif - %if app.config.enable_api: - <li><a target="galaxy_main" href="${h.url_for( controller='/user', action='api_keys' )}">API Keys</a></li> - %endif - </ul> - </div> - </td></tr></table>

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galaxy-dist commit c472ac58348b: lims: added search by request state to find samples page
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1283287548 14400 # Node ID c472ac58348b0cd6d7e2040e4c5b2bfb4f42724e # Parent 568f8d3854e8fcae7f78fbe906971a2369c65c33 lims: added search by request state to find samples page --- a/templates/requests/common/find.mako +++ b/templates/requests/common/find.mako @@ -55,8 +55,8 @@ <form name="find_request" id="find_request" action="${h.url_for( controller='requests_common', action='find', cntrller=cntrller)}" method="post" ><div class="form-row"><label>Find in sequencing requests in state:</label> - <select name="select_search_type"> - <option value="In-Progress" selected>In-Progress</option> + <select name="request_state"> + <option value="In Progress" selected>In-Progress</option><option value="Complete">Complete</option><option value="Both">Both</option></select> --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -1265,6 +1265,12 @@ class RequestsCommon( BaseController, Us status = params.get( 'status', 'done' ) search_string = kwd.get( 'search_string', '' ) search_type = params.get( 'search_type', '' ) + if params.get( 'request_state', 'In Progress' ) == 'Both': + request_states = ['In Progress', 'Complete'] + else: + request_states = [params.get( 'request_state', 'In Progress' )] + + samples_list = [] results = '' if params.get('go_button', '') == 'Go': @@ -1280,10 +1286,15 @@ class RequestsCommon( BaseController, Us .all() if cntrller == 'requests': for s in samples: - if s.request.user.id == trans.user.id: + if s.request.user.id == trans.user.id \ + and s.request.state() in request_states\ + and not s.request.deleted: samples_list.append(s) elif cntrller == 'requests_admin': - samples_list = samples + for s in samples: + if not s.request.deleted \ + and s.request.state() in request_states: + samples_list.append(s) results = 'There are %i sequencing requests matching the search parameters.' % len(samples_list) return trans.fill_template( '/requests/common/find.mako', cntrller=cntrller,

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galaxy-dist commit d9276a4a775a: lims: added 'find samples' feature
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1283286358 14400 # Node ID d9276a4a775a7582a51cedab7b7b2b315109c53f # Parent ff9b7abb6b60850b014496b8756fef1f4440c0d7 lims: added 'find samples' feature - basic search using sample name and barcode implemented - Added menu items in masthead and admin menu --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -116,6 +116,7 @@ <div class="toolSectionBg"><div class="toolTitle"><a href="${h.url_for( controller='requests_admin', action='manage_request_types' )}" target="galaxy_main">Manage request types</a></div><div class="toolTitle"><a href="${h.url_for( controller='requests_admin', action='list')}" target="galaxy_main">Manage requests</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='requests_common', action='find', cntrller='requests_admin')}" target="galaxy_main">Find samples</a></div></div></div></div> --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -1253,5 +1253,49 @@ class RequestsCommon( BaseController, Us dataset_files=sample.datasets, message=message, status=status, files=[], folder_path=folder_path ) + # + # Find sequencing requests & samples + # + @web.expose + @web.require_admin + def find( self, trans, **kwd ): + params = util.Params( kwd ) + cntrller = params.get( 'cntrller', 'requests' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + search_string = kwd.get( 'search_string', '' ) + search_type = params.get( 'search_type', '' ) + samples_list = [] + results = '' + if params.get('go_button', '') == 'Go': + if search_type == 'bar_code': + samples = trans.sa_session.query( trans.app.model.Sample ) \ + .filter( and_( trans.app.model.Sample.table.c.deleted==False, + trans.app.model.Sample.table.c.bar_code.like(search_string) ) )\ + .all() + elif search_type == 'name': + samples = trans.sa_session.query( trans.app.model.Sample ) \ + .filter( and_( trans.app.model.Sample.table.c.deleted==False, + trans.app.model.Sample.table.c.name.like(search_string) ) )\ + .all() + if cntrller == 'requests': + for s in samples: + if s.request.user.id == trans.user.id: + samples_list.append(s) + elif cntrller == 'requests_admin': + samples_list = samples + results = 'There are %i sequencing requests matching the search parameters.' % len(samples_list) + return trans.fill_template( '/requests/common/find.mako', + cntrller=cntrller, + samples=samples_list, + results=results ) + + + + + + + + --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -82,6 +82,14 @@ class RequestsGrid( grids.Grid ): class UserColumn( grids.TextColumn ): def get_value(self, trans, grid, request): return request.user.email + def sort( self, query, ascending ): + """ Sort column using case-insensitive alphabetical sorting on item's username. """ + if ascending: + query = query.order_by( func.lower ( self.model_class.email ).asc() ) + else: + query = query.order_by( func.lower( self.model_class.email ).desc() ) + return query + # Grid definition title = "Sequencing Requests" template = "admin/requests/grid.mako" @@ -119,12 +127,14 @@ class RequestsGrid( grids.Grid ): link=( lambda item: iff( item.deleted, None, dict( operation="events", id=item.id ) ) ), ), UserColumn( "User", - #key='user.email', - model_class=model.Request) + #key='owner', + model_class=model.User + #filterable="advanced" + ) ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1] ], + cols_to_filter=[ columns[0], columns[1], columns[6] ], key="free-text-search", visible=False, filterable="standard" ) ) --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -41,7 +41,8 @@ <a>Lab</a><div class="submenu"><ul> - <li><a href="${h.url_for( controller='/requests', action='index' )}">Sequencing Requests</a></li> + <li><a href="${h.url_for( controller='/requests', action='index' )}">Sequencing requests</a></li> + <li><a href="${h.url_for( controller='/requests_common', action='find', cntrller='requests' )}">Find samples</a></li><li><a target="_blank" href="${app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" )}">Help</a></li></ul></div>

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galaxy-dist commit 65edd8e2a3a8: Fix for pdfnup blathering to stdout causing buildbot to barf
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User fubar: ross Lazarus at gmail period com # Date 1283257544 14400 # Node ID 65edd8e2a3a8872252d9008ad2fe9dee7cbd5856 # Parent 7cc9329fd895049827d1bf5436f6aa11bf9d30ed Fix for pdfnup blathering to stdout causing buildbot to barf Small adjustment to file size delta for rgManQQ --- a/tools/rgenetics/rgManQQ.xml +++ b/tools/rgenetics/rgManQQ.xml @@ -44,9 +44,9 @@ <param name='grey' value='0' /><output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='30'><extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size" - delta = "4000"/> + delta = "10000"/><extra_files type="file" name='Allelep_qqplot.png' value='rgtestouts/rgManQQ/Allelep_qqplot.png' compare="sim_size" - delta = "4000" /> + delta = "10000" /><extra_files type="file" name='rgManQQtest1.R' value='rgtestouts/rgManQQ/rgManQQtest1.R' compare="diff" lines_diff="160"/></output></test> --- a/tools/rgenetics/rgManQQ.py +++ b/tools/rgenetics/rgManQQ.py @@ -52,6 +52,7 @@ manhattan = function(chrom=NULL,offset=N lastbase=0 chrlist = unique(d$CHR) nchr = length(chrlist) # may be any number? + if (nchr < 2) { for (x in c(1:nchr)) { i = chrlist[x] # need the chrom number - may not == index if (x == 1) { # first time @@ -62,8 +63,16 @@ manhattan = function(chrom=NULL,offset=N d[d$CHR==i, ]$pos=d[d$CHR==i, ]$BP+lastbase } ticks=c(ticks, d[d$CHR==i, ]$pos[floor(length(d[d$CHR==i, ]$pos)/2)+1]) - } - ticklim=c(min(d$pos),max(d$pos)) + ticklim=c(min(d$pos),max(d$pos)) + } + } else { # nchr >= 2 + last = max(offset) + first = min(offset) + ticks = first + t = (last-first)/9 # units per tick + for (x in c(1:9)) ticks = c(ticks,round(x*t)) + ticklim = c(first,last) + } # else if (grey) {mycols=rep(c("gray10","gray60"),max(d$CHR)) } else { mycols=rep(coloursTouse,max(d$CHR)) --- a/tools/rgenetics/rgQC.py +++ b/tools/rgenetics/rgQC.py @@ -270,6 +270,8 @@ def makePlots(markers=[],subjects=[],new rpy.r.dev_off() + fdsto,stofile = tempfile.mkstemp() + sto = open(stofile,'w') import rpy # delay to avoid rpy stdout chatter replacing galaxy file blurb mog = 'mogrify' pdfnup = 'pdfnup' @@ -368,7 +370,7 @@ def makePlots(markers=[],subjects=[],new expl = 'All %s QC Plots joined into a single pdf' % basename vcl = '%s %s --outfile %s ' % (pdfjoin,filestojoin, fullafname) # make single page pdf - x=subprocess.Popen(vcl,shell=True,cwd=newfpath) + x=subprocess.Popen(vcl,shell=True,cwd=newfpath,stderr=sto,stdout=sto) retval = x.wait() row = [expl,afname,fullafname] html.insert(0,row) # last rather than second @@ -377,15 +379,17 @@ def makePlots(markers=[],subjects=[],new expl = 'All %s QC Plots %d by %d to a page' % (basename,nup,nup) vcl = '%s %s --nup %dx%d --frame true --outfile %s' % (pdfnup,afname,nup,nup,fullnfname) # make thumbnail images - x=subprocess.Popen(vcl,shell=True,cwd=newfpath) + x=subprocess.Popen(vcl,shell=True,cwd=newfpath,stderr=sto,stdout=sto) retval = x.wait() row = [expl,nfname,fullnfname] html.insert(1,row) # this goes second vcl = '%s -format jpg -resize %s %s' % (mog, mogresize, os.path.join(newfpath,'*.pdf')) # make thumbnail images - x=subprocess.Popen(vcl,shell=True,cwd=newfpath) + x=subprocess.Popen(vcl,shell=True,cwd=newfpath,stderr=sto,stdout=sto) retval = x.wait() - return html # elements for an ordered list of urls or whatever.. + sto.close() + cruft = open(stofile,'r').readlines() + return html,cruft # elements for an ordered list of urls or whatever.. def RmakePlots(markers=[],subjects=[],newfpath='.',basename='test',nbreaks='100',nup=3,height=8,width=10,rexe=''): @@ -1282,7 +1286,7 @@ if __name__ == "__main__": s = '## starting plotpage, newfpath=%s,m=%s,s=%s/n' % (newfpath,markers[:2],subjects[:2]) alogf.write(s) print s - plotpage = makePlots(markers=markers,subjects=subjects,newfpath=newfpath, + plotpage,cruft = makePlots(markers=markers,subjects=subjects,newfpath=newfpath, basename=basename,nbreaks=nbreaks,height=10,width=8,rgbin=rgbin) #plotpage = RmakePlots(markers=markers,subjects=subjects,newfpath=newfpath,basename=basename,nbreaks=nbreaks,rexe=rexe) @@ -1343,6 +1347,8 @@ if __name__ == "__main__": lf.write('\n'.join(html)) lf.write('<h4>QC run log contents</h4>') lf.write('<pre>%s</pre>' % (''.join(llog))) # plink logs + if len(cruft) > 0: + lf.write('<h2>Blather from pdfnup follows:</h2><pre>%s</pre>' % (''.join(cruft))) # pdfnup lf.write('%s\n<hr>\n' % galhtmlpostfix) lf.close()

1 0

galaxy-dist commit b19a56845706: Repacked workflow editor.
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannonbaker(a)me.com> # Date 1283270339 14400 # Node ID b19a56845706a85e5124bd2dd26788752db9c8ef # Parent 1cd9009036f729c8d36fe40db6cbfd6508c3a635 Repacked workflow editor. --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var c in this.datatypes){for(var b in a.datatypes){if(a.datatypes[b]=="input"||issubtype(a.datatypes[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_col or="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a -k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)) .redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClas s("input-terminal-active");return i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);( function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;this.tooltip=g.tooltip?g.tooltip:"";this.annotation=g.annotation;this.post_job_actions=g.post_job_actions;this.workflow_outputs=g.workflow_outputs;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outpu ts,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j))});workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;this.post_job_actions=$.parseJSON(f.post_job_actions);if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0]. terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this .nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(h,i){g[i.name]=null;$.each(i.connectors,function(j,k){g[i.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={job_id:h.id,action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a. steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},no de_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pa d;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(t his).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+image_path+"/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",image_path+"/delete_icon_dark.png")},function(){$(this).attr("src",image_path+"/delete_icon .png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollP anel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManag er.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left) ,i.height()-(g.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top /l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.act ion_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(t his.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind ("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){workflow.check_changes_in_active_form();v ar i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");return i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:fun ction(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;this.tooltip=g.tooltip?g.tooltip:"";this.annotation=g.annotation;this.post_job_actions=g.post_job_actions;this.workflow_outputs=g.workflow_outputs;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal in put-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j))});workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;this.post_job_actions=$.parseJSON(f.post_job_actions);if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div. input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_fo rm_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(h,i){g[i.name]=null;$.each(i.connectors,function(j,k){g[i.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={job_id:h.id,action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id ,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},clear_active_node:function(){if(this.active_node){this.active_node.mak e_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in lev el_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h ,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+image_path+"/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i .append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",image_path+"/delete_icon_dark.png")},function(){$(this).attr("src",image_path+"/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.t erminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=thi s;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).of fsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g *d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -44,7 +44,7 @@ def js( *args ): TODO: This has a hardcoded "?v=X" to defeat caching. This should be done in a better way. """ - return "\n".join( [ javascript_include_tag( "/static/scripts/" + name + ".js?v=6" ) for name in args ] ) + return "\n".join( [ javascript_include_tag( "/static/scripts/" + name + ".js?v=7" ) for name in args ] ) # Hashes

1 0

galaxy-dist commit 6b2dffb999d8: Fix for temporary name generation - now use mkstemp for the name and keep the filename
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User fubar: ross Lazarus at gmail period com # Date 1283235958 14400 # Node ID 6b2dffb999d8595d410dc299fb512b76c35be39e # Parent b7e13932acf9e58dee2bb3f2799e7e27402ffc63 Fix for temporary name generation - now use mkstemp for the name and keep the filename at the end of the temporary name for tools where the extension matters in tests --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -616,6 +616,16 @@ class TwillTestCase( unittest.TestCase ) hid = elem.get('hid') hids.append(hid) return hids + + def makeTfname(self, fname=None): + """ + safe temp name - preserve the file extension for tools that interpret it + """ + suffix = os.path.split(fname)[-1] # ignore full path + fd,temp_prefix = tempfile.mkstemp(prefix='tmp',suffix=suffix) + return temp_prefix + + def verify_dataset_correctness( self, filename, hid=None, wait=True, maxseconds=120, attributes=None ): """Verifies that the attributes and contents of a history item meet expectations""" if wait: @@ -645,7 +655,7 @@ class TwillTestCase( unittest.TestCase ) raise AssertionError( errmsg ) else: local_name = self.get_filename( filename ) - temp_name = self.get_filename( '%s_temp' % filename ) #This is a terrible way to generate a temp name + temp_name = self.makeTfname(fname = filename) self.home() self.visit_page( "display?hid=" + hid ) data = self.last_page() @@ -691,7 +701,7 @@ class TwillTestCase( unittest.TestCase ) local_name = self.get_filename( file_name ) if base_name is None: base_name = os.path.split(file_name)[-1] - temp_name = self.get_filename( '%s_temp' % file_name ) #This is a terrible way to generate a temp name + temp_name = self.makeTfname(fname = base_name) self.visit_url( "%s/datasets/%s/display/%s" % ( self.url, self.security.encode_id( hda_id ), base_name ) ) data = self.last_page() file( temp_name, 'wb' ).write( data ) @@ -720,7 +730,7 @@ class TwillTestCase( unittest.TestCase ) errmsg += str( err ) raise AssertionError( errmsg ) finally: - os.remove( temp_name ) + os.remove( temp_name ) def is_zipped( self, filename ): if not zipfile.is_zipfile( filename ): @@ -728,7 +738,7 @@ class TwillTestCase( unittest.TestCase ) return True def is_binary( self, filename ): - temp = open( temp_name, "U" ) + temp = open( filename, "U" ) # why is this not filename? Where did temp_name come from lineno = 0 for line in temp: lineno += 1

1 0

galaxy-dist commit b7e13932acf9: Issue #380: Properly handle -n and -v options in Bowtie
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1283231072 14400 # Node ID b7e13932acf9e58dee2bb3f2799e7e27402ffc63 # Parent 1cd9009036f729c8d36fe40db6cbfd6508c3a635 Issue #380: Properly handle -n and -v options in Bowtie --- a/tools/sr_mapping/bowtie_wrapper.py +++ b/tools/sr_mapping/bowtie_wrapper.py @@ -120,6 +120,7 @@ def __main__(): parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' ) (options, args) = parser.parse_args() stdout = '' + # make temp directory for placement of indices and copy reference file there if necessary tmp_index_dir = tempfile.mkdtemp() # get type of data (solid or solexa) @@ -190,7 +191,7 @@ def __main__(): # clean up temp dir if os.path.exists( tmp_index_dir ): shutil.rmtree( tmp_index_dir ) - stop_err( 'Something is wrong with the indexing parameters and the indexing and alignment could not be run\n' + str( e ) ) + stop_err( "Something is wrong with the indexing parameters and the indexing and alignment could not be run. Make sure you don't have any non-numeric values where they should be numeric.\n" + str( e ) ) ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir ) ref_file_name = ref_file.name ref_file.close() @@ -259,7 +260,7 @@ def __main__(): trimL = '-3 %s' % options.trimL else: trimL = '' - if options. mismatchSeed != 'None' and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \ + if options.mismatchSeed != 'None' and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \ or options.mismatchSeed == '2' or options.mismatchSeed == '3'): mismatchSeed = '-n %s' % options.mismatchSeed else: @@ -276,7 +277,7 @@ def __main__(): rounding = '--nomaqround' else: rounding = '' - if options.maqSoapAlign != '-1': + if options.maqSoapAlign != '-1' and int( options.maqSoapAlign ) >= 0: maqSoapAlign = '-v %s' % options.maqSoapAlign else: maqSoapAlign = ''

1 0

galaxy-dist commit 7cc9329fd895: Fixes to some rgenetics tests and test outputs
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User fubar: ross Lazarus at gmail period com # Date 1283236053 14400 # Node ID 7cc9329fd895049827d1bf5436f6aa11bf9d30ed # Parent 6b2dffb999d8595d410dc299fb512b76c35be39e Fixes to some rgenetics tests and test outputs Some odd bugs in the new version of ggplot2 in R Fixes to the Rrun function in rgutils Binary file test-data/rgtestouts/rgManQQ/Allelep_manhattan.png has changed --- a/tools/rgenetics/rgManQQ.py +++ b/tools/rgenetics/rgManQQ.py @@ -75,25 +75,25 @@ manhattan = function(chrom=NULL,offset=N # only makes sense if genome wide is assumed - we could have a fine mapping region? if (annotate) d.annotate=d[as.numeric(substr(d$SNP,3,100)) %in% SNPlist, ] - plot=qplot(pos,logp,data=d, ylab=expression(-log[10](italic(p))) , colour=factor(CHR)) - plot=plot+scale_x_continuous(name="Chromosome", breaks=ticks, labels=(unique(d$CHR))) - plot=plot+scale_y_continuous(limits=c(0,maxy), breaks=1:maxy, labels=1:maxy) - plot=plot+scale_colour_manual(value=mycols) - if (annotate) plot=plot + geom_point(data=d.annotate, colour=I("green3")) - plot=plot + opts(legend.position = "none") - plot=plot + opts(title=title) - plot=plot+opts( + manplot=qplot(pos,logp,data=d, ylab=expression(-log[10](italic(p))) , colour=factor(CHR)) + manplot=manplot+scale_x_continuous(name="Chromosome", breaks=ticks, labels=(unique(d$CHR))) + manplot=manplot+scale_y_continuous(limits=c(0,maxy), breaks=1:maxy, labels=1:maxy) + manplot=manplot+scale_colour_manual(value=mycols) + if (annotate) { manplot=manplot + geom_point(data=d.annotate, colour=I("green3")) } + manplot=manplot + opts(legend.position = "none") + manplot=manplot + opts(title=title) + manplot=manplot+opts( panel.background=theme_blank(), axis.text.x=theme_text(size=size.x.labels, colour="grey50"), axis.text.y=theme_text(size=size.y.labels, colour="grey50"), axis.ticks=theme_segment(colour=NA) ) - #plot = plot + opts(panel.grid.y.minor=theme_blank(),panel.grid.y.major=theme_blank()) - #plot = plot + opts(panel.grid.major=theme_blank()) + #manplot = manplot + opts(panel.grid.y.minor=theme_blank(),panel.grid.y.major=theme_blank()) + #manplot = manplot + opts(panel.grid.major=theme_blank()) - if (suggestiveline) plot=plot+geom_hline(yintercept=suggestiveline,colour="blue", alpha=I(1/3)) - if (genomewideline) plot=plot+geom_hline(yintercept=genomewideline,colour="red") - plot + if (suggestiveline) manplot=manplot+geom_hline(yintercept=suggestiveline,colour="blue", alpha=I(1/3)) + if (genomewideline) manplot=manplot+geom_hline(yintercept=genomewideline,colour="red") + manplot } else { stop("Make sure your data frame contains columns CHR, BP, and P") } @@ -110,12 +110,12 @@ qq = function(pvector, title=NULL, spart # ylab=expression(Observed~~-log[10](italic(p))), xlim=c(0,max(e)), ylim=c(0,max(e))) # lines(e,e,col="red") #You'll need ggplot2 installed to do the rest - plot=qplot(e,o, xlim=c(0,max(e)), ylim=c(0,max(o))) + stat_abline(intercept=0,slope=1, col="red") - plot=plot+opts(title=title) - plot=plot+scale_x_continuous(name=expression(Expected~~-log[10](italic(p)))) - plot=plot+scale_y_continuous(name=expression(Observed~~-log[10](italic(p)))) + qq=qplot(e,o, xlim=c(0,max(e)), ylim=c(0,max(o))) + stat_abline(intercept=0,slope=1, col="red") + qq=qq+opts(title=title) + qq=qq+scale_x_continuous(name=expression(Expected~~-log[10](italic(p)))) + qq=qq+scale_y_continuous(name=expression(Observed~~-log[10](italic(p)))) if (spartan) plot=plot+opts(panel.background=theme_rect(col="grey50"), panel.grid.minor=theme_blank()) - plot + qq } """ @@ -140,6 +140,7 @@ if (plen > 0) { mytitle = paste('p=',cname,', ',title,sep='') myfname = chartr(' ','_',cname) myqqplot = qq(rawd[,pvalscolumn],title=mytitle) + ggsave(filename=paste(myfname,"qqplot.png",sep='_'),myqqplot,width=8,height=11) print(paste('## qqplot on',cname,'done')) if ((chromcolumn > 0) & (offsetcolumn > 0)) { if (doreorder) { @@ -151,13 +152,12 @@ if (plen > 0) { print(paste('## manhattan on',cname,'starting',chromcolumn,offsetcolumn,pvalscolumn)) mymanplot= manhattan(chrom=rawd[,chromcolumn],offset=rawd[,offsetcolumn],pvals=rawd[,pvalscolumn],title=mytitle,grey=grey) print(paste('## manhattan plot on',cname,'done')) - ggsave(file=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=11,height=8,dpi=100) + ggsave(filename=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=11,height=8) } else { print(paste('chrom column =',chromcolumn,'offset column = ',offsetcolumn, 'so no Manhattan plot - supply both chromosome and offset as numerics for Manhattan plots if required')) } - ggsave(file=paste(myfname,"qqplot.png",sep='_'),myqqplot,width=8,height=11,dpi=100) } else { print(paste('pvalue column =',pvalscolumn,'Cannot parse it so no plots possible')) @@ -177,9 +177,10 @@ def doManQQ(input_fname,chrom_col,offset to make them do our bidding - and save the resulting code for posterity this can be called externally, I guess...for QC eg? """ - rcmd = '%s%s' % (rcode,rcode2 % (input_fname,chrom_col,offset_col,pval_cols,title,grey)) rlog,flist = RRun(rcmd=rcmd,title=ctitle,outdir=outdir) + rlog.append('## R script=') + rlog.append(rcmd) return rlog,flist --- a/test-data/rgtestouts/rgManQQ/rgManQQtest1.R +++ b/test-data/rgtestouts/rgManQQ/rgManQQtest1.R @@ -108,7 +108,7 @@ qq = function(pvector, title=NULL, spart if (spartan) plot=plot+opts(panel.background=theme_rect(col="grey50"), panel.grid.minor=theme_blank()) plot } -rgqqMan = function(infile="/share/shared/galaxy/test-data/smallwgaP.xls",chromcolumn=2, offsetcolumn=3, pvalscolumns=c(6,8), +rgqqMan = function(infile="/opt/galaxy/test-data/smallwgaP.xls",chromcolumn=2, offsetcolumn=3, pvalscolumns=c(8), title="rgManQQtest1",grey=0) { rawd = read.table(infile,head=T,sep=' ') dn = names(rawd) @@ -155,4 +155,4 @@ if (plen > 0) { rgqqMan() # execute with defaults as substituted -#R script autogenerated by rgenetics/rgutils.py on 09/05/2010 21:23:26 +#R script autogenerated by rgenetics/rgutils.py on 30/08/2010 04:09:48 --- a/tools/rgenetics/rgGRR.py +++ b/tools/rgenetics/rgGRR.py @@ -78,7 +78,7 @@ class NullDevice: pass tempstderr = sys.stderr # save -sys.stderr = NullDevice() +#sys.stderr = NullDevice() # need to avoid blather about deprecation and other strange stuff from scipy # the current galaxy job runner assumes that # the job is in error if anything appears on sys.stderr --- a/test-data/rgtestouts/rgManQQ/rgManQQtest1.html +++ b/test-data/rgtestouts/rgManQQ/rgManQQtest1.html @@ -15,30 +15,21 @@ <tr><td><a href="Allelep_manhattan.png"><img src="Allelep_manhattan.png" alt="Allelep_manhattan.png hspace="10" width="400"><br>(Click to download image Allelep_manhattan.png)</a></td></tr><tr><td><a href="Allelep_qqplot.png"><img src="Allelep_qqplot.png" alt="Allelep_qqplot.png hspace="10" width="400"><br>(Click to download image Allelep_qqplot.png)</a></td></tr> -<tr><td><a href="Armitagep_manhattan.png"><img src="Armitagep_manhattan.png" alt="Armitagep_manhattan.png hspace="10" width="400"><br>(Click to download image Armitagep_manhattan.png)</a></td></tr> -<tr><td><a href="Armitagep_qqplot.png"><img src="Armitagep_qqplot.png" alt="Armitagep_qqplot.png hspace="10" width="400"><br>(Click to download image Armitagep_qqplot.png)</a></td></tr><tr><td><a href="rgManQQtest1.R">rgManQQtest1.R</a></td></tr> +<tr><td><a href="rgManQQtest1.R.log">rgManQQtest1.R.log</a></td></tr></table><h3>R log follows below</h3><hr><pre> -Loading required package: proto - -Loading required package: grid - Loading required package: reshape Loading required package: plyr -Loading required package: digest +Loading required package: grid -[1] "### 101 values read from /share/shared/galaxy/test-data/smallwgaP.xls read - now running plots" +Loading required package: proto -[1] "## qqplot on Armitagep done" - -[1] "## manhattan on Armitagep starting 2 3 6" - -[1] "## manhattan plot on Armitagep done" +[1] "### 101 values read from /opt/galaxy/test-data/smallwgaP.xls read - now running plots" [1] "## qqplot on Allelep done" @@ -46,8 +37,166 @@ Loading required package: digest [1] "## manhattan plot on Allelep done" +## R script= + +# license not stated so I'm assuming LGPL is ok for my derived work? +# generalised so 3 core fields passed as parameters ross lazarus March 24 2010 for rgenetics +# Originally created as qqman with the following +# attribution: +#-------------- +# Stephen Turner +# http://StephenTurner.us/ +# http://GettingGeneticsDone.blogspot.com/ + +# Last updated: Tuesday, December 22, 2009 +# R code for making manhattan plots and QQ plots from plink output files. +# With GWAS data this can take a lot of memory. Recommended for use on +# 64bit machines only, for now. + +# + +library(ggplot2) + +coloursTouse = c('firebrick','darkblue','goldenrod','darkgreen') +# not too fugly but need a colour expert please... + + +manhattan = function(chrom=NULL,offset=NULL,pvals=NULL, title=NULL, max.y="max", + suggestiveline=0, genomewide=T, size.x.labels=9, size.y.labels=10, annotate=F, SNPlist=NULL,grey=0) { + + if (annotate & is.null(SNPlist)) stop("You requested annotation but provided no SNPlist!") + genomewideline=NULL # was genomewideline=-log10(5e-8) + if (genomewide) { # use bonferroni since might be only a small region? + genomewideline = -log10(0.05/length(pvals)) } + d=data.frame(CHR=chrom,BP=offset,P=pvals) + + #limit to only chrs 1-23? + d=d[d$CHR %in% 1:23, ] + + if ("CHR" %in% names(d) & "BP" %in% names(d) & "P" %in% names(d) ) { + d=na.omit(d) + d=d[d$P>0 & d$P<=1, ] + d$logp = -log10(d$P) + + d$pos=NA + ticks=NULL + lastbase=0 + chrlist = unique(d$CHR) + nchr = length(chrlist) # may be any number? + for (x in c(1:nchr)) { + i = chrlist[x] # need the chrom number - may not == index + if (x == 1) { # first time + d[d$CHR==i, ]$pos=d[d$CHR==i, ]$BP + } else { + lastchr = chrlist[x-1] # previous whatever the list + lastbase=lastbase+tail(subset(d,CHR==lastchr)$BP, 1) + d[d$CHR==i, ]$pos=d[d$CHR==i, ]$BP+lastbase + } + ticks=c(ticks, d[d$CHR==i, ]$pos[floor(length(d[d$CHR==i, ]$pos)/2)+1]) + } + ticklim=c(min(d$pos),max(d$pos)) + if (grey) {mycols=rep(c("gray10","gray60"),max(d$CHR)) + } else { + mycols=rep(coloursTouse,max(d$CHR)) + } + + if (max.y=="max") maxy=ceiling(max(d$logp)) else maxy=max.y + maxy = max(maxy,1.1*genomewideline) + # if (maxy<8) maxy=8 + # only makes sense if genome wide is assumed - we could have a fine mapping region? + if (annotate) d.annotate=d[as.numeric(substr(d$SNP,3,100)) %in% SNPlist, ] + + manplot=qplot(pos,logp,data=d, ylab=expression(-log[10](italic(p))) , colour=factor(CHR)) + manplot=manplot+scale_x_continuous(name="Chromosome", breaks=ticks, labels=(unique(d$CHR))) + manplot=manplot+scale_y_continuous(limits=c(0,maxy), breaks=1:maxy, labels=1:maxy) + manplot=manplot+scale_colour_manual(value=mycols) + if (annotate) { manplot=manplot + geom_point(data=d.annotate, colour=I("green3")) } + manplot=manplot + opts(legend.position = "none") + manplot=manplot + opts(title=title) + manplot=manplot+opts( + panel.background=theme_blank(), + axis.text.x=theme_text(size=size.x.labels, colour="grey50"), + axis.text.y=theme_text(size=size.y.labels, colour="grey50"), + axis.ticks=theme_segment(colour=NA) + ) + #manplot = manplot + opts(panel.grid.y.minor=theme_blank(),panel.grid.y.major=theme_blank()) + #manplot = manplot + opts(panel.grid.major=theme_blank()) + + if (suggestiveline) manplot=manplot+geom_hline(yintercept=suggestiveline,colour="blue", alpha=I(1/3)) + if (genomewideline) manplot=manplot+geom_hline(yintercept=genomewideline,colour="red") + manplot + } else { + stop("Make sure your data frame contains columns CHR, BP, and P") + } +} + + + +qq = function(pvector, title=NULL, spartan=F) { + # Thanks to Daniel Shriner at NHGRI for providing this code for creating expected and observed values + o = -log10(sort(pvector,decreasing=F)) + e = -log10( 1:length(o)/length(o) ) + # you could use base graphics + # plot(e,o,pch=19,cex=0.25, xlab=expression(Expected~~-log[10](italic(p))), + # ylab=expression(Observed~~-log[10](italic(p))), xlim=c(0,max(e)), ylim=c(0,max(e))) + # lines(e,e,col="red") + #You'll need ggplot2 installed to do the rest + qq=qplot(e,o, xlim=c(0,max(e)), ylim=c(0,max(o))) + stat_abline(intercept=0,slope=1, col="red") + qq=qq+opts(title=title) + qq=qq+scale_x_continuous(name=expression(Expected~~-log[10](italic(p)))) + qq=qq+scale_y_continuous(name=expression(Observed~~-log[10](italic(p)))) + if (spartan) plot=plot+opts(panel.background=theme_rect(col="grey50"), panel.grid.minor=theme_blank()) + qq +} +rgqqMan = function(infile="/opt/galaxy/test-data/smallwgaP.xls",chromcolumn=2, offsetcolumn=3, pvalscolumns=c(8), +title="rgManQQtest1",grey=0) { +rawd = read.table(infile,head=T,sep=' ') +dn = names(rawd) +cc = dn[chromcolumn] +oc = dn[offsetcolumn] +nams = c(cc,oc) +plen = length(rawd[,1]) +doreorder=1 +print(paste('###',plen,'values read from',infile,'read - now running plots',sep=' ')) +if (plen > 0) { + for (pvalscolumn in pvalscolumns) { + if (pvalscolumn > 0) + { + cname = names(rawd)[pvalscolumn] + mytitle = paste('p=',cname,', ',title,sep='') + myfname = chartr(' ','_',cname) + myqqplot = qq(rawd[,pvalscolumn],title=mytitle) + print(paste('## qqplot on',cname,'done')) + if ((chromcolumn > 0) & (offsetcolumn > 0)) { + if (doreorder) { + rawd = rawd[do.call(order,rawd[nams]),] + # mmmf - suggested by http://onertipaday.blogspot.com/2007/08/sortingordering-dataframe-according… + # in case not yet ordered + doreorder = 0 + } + print(paste('## manhattan on',cname,'starting',chromcolumn,offsetcolumn,pvalscolumn)) + mymanplot= manhattan(chrom=rawd[,chromcolumn],offset=rawd[,offsetcolumn],pvals=rawd[,pvalscolumn],title=mytitle,grey=grey) + print(paste('## manhattan plot on',cname,'done')) + ggsave(filename=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=11,height=8,dpi=100) + } + else { + print(paste('chrom column =',chromcolumn,'offset column = ',offsetcolumn, + 'so no Manhattan plot - supply both chromosome and offset as numerics for Manhattan plots if required')) + } + ggsave(filename=paste(myfname,"qqplot.png",sep='_'),myqqplot,width=8,height=11,dpi=100) + } + else { + print(paste('pvalue column =',pvalscolumn,'Cannot parse it so no plots possible')) + } + } # for pvalscolumn + } else { print('## Problem - no values available to plot - was there really a chromosome and offset column?') } +} + +rgqqMan() +# execute with defaults as substituted + </pre> -<h3><a href="http://rgenetics.org">Rgenetics</a> tool rgManQQ.py run at 09/05/2010 21:23:34</h3> +<h3><a href="http://rgenetics.org">Rgenetics</a> tool rgManQQ.py run at 30/08/2010 20:46:51</h3></div></body></html> --- a/tools/rgenetics/rgManQQ.xml +++ b/tools/rgenetics/rgManQQ.xml @@ -42,14 +42,10 @@ <param name='chrom_col' value='1' /><param name='offset_col' value='2' /><param name='grey' value='0' /> - <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='17'> - <extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size" - delta = "4000" /> - <extra_files type="file" name='Allelep_qqplot.png' value='rgtestouts/rgManQQ/Allelep_qqplot.png' compare="sim_size" - delta = "4000" /> - <extra_files type="file" name='Armitagep_manhattan.png' value='rgtestouts/rgManQQ/Armitagep_manhattan.png' compare="sim_size" + <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='30'> + <extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size" delta = "4000"/> - <extra_files type="file" name='Armitagep_qqplot.png' value='rgtestouts/rgManQQ/Armitagep_qqplot.png' compare="sim_size" + <extra_files type="file" name='Allelep_qqplot.png' value='rgtestouts/rgManQQ/Allelep_qqplot.png' compare="sim_size" delta = "4000" /><extra_files type="file" name='rgManQQtest1.R' value='rgtestouts/rgManQQ/rgManQQtest1.R' compare="diff" lines_diff="160"/></output> --- a/tools/rgenetics/rgutils.py +++ b/tools/rgenetics/rgutils.py @@ -122,32 +122,36 @@ def RRun(rcmd=[],outdir=None,title='myR' tempout=False rname = '%s.R' % title stoname = '%s.R.log' % title + cwd = os.getcwd() if outdir: # want a specific path try: os.makedirs(outdir) # might not be there yet... except: pass - else: - tempout = True - outdir = tempfile.mkdtemp(prefix=title) + os.chdir(outdir) if type(rcmd) == type([]): script = '\n'.join(rcmd) else: # string script = rcmd sto = file(stoname,'w') - rscriptname = os.path.join(outdir,rname) - rscript = file(rscriptname,'w') + rscript = file(rname,'w') rscript.write(script) rscript.write('\n#R script autogenerated by rgenetics/rgutils.py on %s\n' % timenow()) rscript.close() - vcl = '%s --slave --vanilla < %s' % (rexe,rscriptname) - x = subprocess.Popen(vcl,shell=True,stderr=sto,stdout=sto,cwd=outdir) + vcl = '%s --slave --vanilla < %s' % (rexe,rname) + if outdir: + x = subprocess.Popen(vcl,shell=True,stderr=sto,stdout=sto,cwd=outdir) + else: + x = subprocess.Popen(vcl,shell=True,stderr=sto,stdout=sto) retval = x.wait() sto.close() rlog = file(stoname,'r').readlines() if retval <> 0: rlog.insert(0,'Nonzero exit code = %d' % retval) # indicate failure - flist = os.listdir(outdir) + if outdir: + flist = os.listdir(outdir) + else: + flist = os.listdir(os.getcwd()) flist.sort flist = [(x,x) for x in flist] for i,x in enumerate(flist): @@ -155,16 +159,8 @@ def RRun(rcmd=[],outdir=None,title='myR' flist[i] = (x,'R script for %s' % title) elif x == stoname: flist[i] = (x,'R log for %s' % title) - if tidy and tempout: # we used a temp one - fix that - flist = os.listdir(outdir) - for f in flist: - if os.path.isdir(f): - flist2 = os.listdir(f) - for f2 in flist2: - os.unlink(os.path.abspath(f2)) - else: - os.unlink(os.path.abspath(f)) - os.rmdir(outdir) + if outdir: + os.chdir(cwd) return rlog,flist # for html layout def runPlink(bfn='bar',ofn='foo',logf=None,plinktasks=[],cd='./',vclbase = []): --- a/tools/rgenetics/rgtest.sh +++ b/tools/rgenetics/rgtest.sh @@ -41,7 +41,7 @@ CL="python $TOOLPATH/$TOOL.py "$INPATH/s #python /opt/galaxy/tools/rgenetics/rgManQQ.py /opt/galaxy/test-data/smallwgaP.xls rgManQQtest1 #/opt/galaxy/test-data/rgtestouts/rgManQQ/rgManQQtest1.html /opt/galaxy/test-data/rgtestouts/rgManQQ 1 2 5,7 echo "Testing $TOOL using $CL" -python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 5,7 0 +python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 7 0 TOOL="rgfakePhe" NPRE=${TOOL}test1 OUTPATH="$OROOT/$TOOL" Binary file test-data/rgtestouts/rgManQQ/Allelep_qqplot.png has changed

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