Hi Kip, For the time being we are using this method to achieve the same result, although its not as nice as just having a multi-select menu in the form: <command> ... $input1 #for $r in $add_inputs $r.$input2 #end for ... </command> In <inputs>: <param name="input1" type="data"/> <repeat name="add_inputs"> <param name="input2" type="data" /> </repeat> best, Leandro On Thu, Jun 30, 2011 at 4:52 PM, Kip Bodi <kip.bodi(a)tufts.edu&gt; wrote: > Sorry, I tried to edit that, to make it simpler, but missed the <param> > block. The 'name' does match the one in the 'command' on my end > (list_of_items_in_history). > > On Thu, Jun 30, 2011 at 10:45 AM, Kip Bodi <kip.bodi(a)tufts.edu&gt; wrote: >> >> Hi all, >> >> I'm having the same problem. I have a script that tries to take several >> history data sets as a single input: >> >> <command interpreter="perl">aggregate.pl --out $outfile >> $list_of_items_in_history</command> >> >> <inputs> >> <param format="txt" name="fitness_tables" type="data" multiple="true" >> label="Fitness score table, per site"/> >> </inputs> >> >> <outputs> >> <data format="tabular" name="outfile" /> >> </outputs> >> >> If I select only one history item it works, but if I press 'ctrl' to >> select multiple items, it fails: >> >> File >> '/storage/apps/galaxy_dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', >> line 364 in respond >> app_iter = self.application(environ, detect_start_response) >> File '/usr/lib/python2.6/site-packages/paste/debug/prints.py', line 106 in >> __call__ >> environ, self.app) >> File '/usr/lib/python2.6/site-packages/paste/wsgilib.py', line 543 in >> intercept_output >> app_iter = application(environ, replacement_start_response) >> File '/usr/lib/python2.6/site-packages/paste/recursive.py', line 80 in >> __call__ >> return self.application(environ, start_response) >> File '/usr/lib/python2.6/site-packages/paste/httpexceptions.py', line 633 >> in __call__ >> return self.application(environ, start_response) >> File '/storage/apps/galaxy_dist/lib/galaxy/web/framework/base.py', line >> 145 in __call__ >> body = method( trans, **kwargs ) >> File >> '/storage/apps/galaxy_dist/lib/galaxy/web/controllers/tool_runner.py', line >> 68 in index >> template, vars = tool.handle_input( trans, params.__dict__ ) >> File '/storage/apps/galaxy_dist/lib/galaxy/tools/__init__.py', line 979 in >> handle_input >> _, out_data = self.execute( trans, incoming=params, history=history ) >> File '/storage/apps/galaxy_dist/lib/galaxy/tools/__init__.py', line 1271 >> in execute >> return self.tool_action.execute( self, trans, incoming=incoming, >> set_output_hid=set_output_hid, history=history, **kwargs ) >> File '/storage/apps/galaxy_dist/lib/galaxy/tools/actions/__init__.py', >> line 360 in execute >> for name, value in tool.params_to_strings( incoming, trans.app >> ).iteritems(): >> File '/storage/apps/galaxy_dist/lib/galaxy/tools/__init__.py', line 1274 >> in params_to_strings >> return params_to_strings( self.inputs, params, app ) >> File '/storage/apps/galaxy_dist/lib/galaxy/tools/parameters/__init__.py', >> line 79 in params_to_strings >> value = params[ key ].value_to_basic( value, app ) >> File '/storage/apps/galaxy_dist/lib/galaxy/tools/parameters/basic.py', >> line 110 in value_to_basic >> return self.to_string( value, app ) >> File '/storage/apps/galaxy_dist/lib/galaxy/tools/parameters/basic.py', >> line 1457 in to_string >> return value.id >> AttributeError: 'list' object has no attribute 'id' >> >> Is using multiple history items as a single input not currently supported, >> or is there something else I'm doing wrong? >> >> Cheers, >> >> Kip >> >> On Thu, Jun 9, 2011 at 7:05 AM, Leandro Hermida >> <softdev(a)leandrohermida.com&gt; wrote: >>> >>> Hi again, >>> >>> Sorry to ping again about this, just very interested in knowing if >>> this is a missing feature in Galaxy or if I had configured something >>> wrong. >>> >>> Is it possible in Galaxy to have a tool with a multiple="true" input >>> dataset parameter? It doesn't seem so? >>> >>> best, >>> Leandro >>> >>> >>> On Tue, May 24, 2011 at 1:31 PM, Leandro Hermida >>> <softdev(a)leandrohermida.com&gt; wrote: >>> > Hi Nate, >>> > >>> > Thanks for the ping, have fun at the conference! >>> > On Tue, May 24, 2011 at 11:22 AM, Nate Coraor <nate(a)bx.psu.edu&gt; wrote: >>> >> >>> >> Hi Leandro, >>> >> >>> >> The Galaxy Team has recently been preparing for and traveling in >>> >> advance >>> >> of the Galaxy Community Conference, which begins today. Unfortunately >>> >> I >>> >> don't have an answer for you, but when we're all back at work next >>> >> week, >>> >> someone should be able to respond. >>> >> >>> >> Thanks, >>> >> --nate >>> >> >>> >> Leandro Hermida wrote: >>> >> > Hi again, >>> >> > >>> >> > Very sorry to ask again, just gotten no repsonse, but is this a >>> >> > Galaxy >>> >> > bug >>> >> > or does anyone have a functioning tool that takes multiple datasets >>> >> > as >>> >> > an >>> >> > input parameter??? i.e. >>> >> > >>> >> > <param type="data" multiple="true" ... /> >>> >> > >>> >> > regards, >>> >> > Leandro >>> >> > >>> >> > On Thu, May 19, 2011 at 7:15 PM, Leandro Hermida >>> >> > <softdev(a)leandrohermida.com >>> >> > > wrote: >>> >> > >>> >> > > Hi again, >>> >> > > >>> >> > > I tried changing the format to txt and tabular which I have other >>> >> > > datasets >>> >> > > in my history and still the same error and stack trace in Galaxy. >>> >> > > >>> >> > > Is it possible at all to have a select multiple of datasets as an >>> >> > > input >>> >> > > parameter?? >>> >> > > >>> >> > > best, >>> >> > > Leandro >>> >> > > >>> >> > > >>> >> > > On Thu, May 19, 2011 at 6:59 PM, Leandro Hermida < >>> >> > > softdev(a)leandrohermida.com&gt; wrote: >>> >> > > >>> >> > >> Hi Galaxy developers, >>> >> > >> >>> >> > >> Something seems maybe to be wrong with the format="html" type... >>> >> > >> I >>> >> > >> forgot >>> >> > >> to add before that my tool input param the format="html" >>> >> > >> attribute: >>> >> > >> >>> >> > >> <param type="data" multiple="true" format="html" name="input1" /> >>> >> > >> >>> >> > >> In another tool I have it outputs format="html" and this works >>> >> > >> and >>> >> > >> displays in Galaxy just fine. I would like to use multiple of >>> >> > >> these >>> >> > >> output >>> >> > >> datasets in my history as the input for this other tool but >>> >> > >> something >>> >> > >> seems >>> >> > >> to be wrong if you try to do this? >>> >> > >> >>> >> > >> a bit lost, >>> >> > >> Leandro >>> >> > >> >>> >> > >> >>> >> > >> On Thu, May 19, 2011 at 3:30 PM, Leandro Hermida < >>> >> > >> softdev(a)leandrohermida.com&gt; wrote: >>> >> > >> >>> >> > >>> Hi, >>> >> > >>> >>> >> > >>> I have a tool where the input is multi-select of datasets, e.g.: >>> >> > >>> >>> >> > >>> <param type="data" multiple="true" name="input1" /> >>> >> > >>> >>> >> > >>> I tested it to see what it would pass to my command and I get >>> >> > >>> the >>> >> > >>> following debug page and error in Galaxy: >>> >> > >>> >>> >> > >>> AttributeError: 'list' object has no attribute 'missing_meta' >>> >> > >>> >>> >> > >>> The last part of the stack trace looks like: >>> >> > >>> >>> >> > >>> >> validator.validate( value, history ) >>> >> > >>> Module galaxy.tools.parameters.validation:185 in validate >>> >> > >>> >>> >> > >>> history <galaxy.model.History object at 0xb8ea190> >>> >> > >>> self >>> >> > >>> <galaxy.tools.parameters.validation.MetadataValidator >>> >> > >>> object >>> >> > >>> at 0xb8e6250> >>> >> > >>> value [<galaxy.model.HistoryDatasetAssociation object at >>> >> > >>> 0xa255550>, >>> >> > >>> <galaxy.model.HistoryDataset ... Association object at >>> >> > >>> 0xb8ea210>] >>> >> > >>> >>> >> > >>> >> if value and value.missing_meta( check = self.check, skip = >>> >> > >>> >> self.skip >>> >> > >>> ): >>> >> > >>> AttributeError: 'list' object has no attribute 'missing_meta' >>> >> > >>> >>> >> > >>> What am I doing wrong? >>> >> > >>> >>> >> > >>> regards, >>> >> > >>> Leandro >>> >> > >>> >>> >> > >>> >>> >> > >> >>> >> > > >>> >> >>> >> > ___________________________________________________________ >>> >> > Please keep all replies on the list by using "reply all" >>> >> > in your mail client. To manage your subscriptions to this >>> >> > and other Galaxy lists, please use the interface at: >>> >> > >>> >> > http://lists.bx.psu.edu/ >>> >> >>> > >>> > >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >> >> >> -- >> Kip Lord Bodi Jr. >> Tufts University School of Medicine >> 136 Harrison Avenue, South Cove 502 >> Boston, MA 02118 >> 617-636-3763 >> kip.bodi(a)tufts.edu >> www.tucf.org | genomics.med.tufts.edu > > > > -- > Kip Lord Bodi Jr. > Tufts University School of Medicine > 136 Harrison Avenue, South Cove 502 > Boston, MA 02118 > 617-636-3763 > kip.bodi(a)tufts.edu > www.tucf.org | genomics.med.tufts.edu >