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