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
<soft...@leandrohermida.com>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
> <soft...@leandrohermida.com> wrote:
> > Hi Nate,
> >
> > Thanks for the ping, have fun at the conference!
> > On Tue, May 24, 2011 at 11:22 AM, Nate Coraor <n...@bx.psu.edu> 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
> >> > <soft...@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 <
> >> > > soft...@leandrohermida.com> 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 <
> >> > >> soft...@leandrohermida.com> 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/
> >>
> >
> >
>
> ___________________________________________________________
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>  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.b...@tufts.edu
www.tucf.org | genomics.med.tufts.edu
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