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.b...@tufts.edu> 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 <
> 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/
>> >>
>> >
>> >
>>
>> ___________________________________________________________
>> 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.b...@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.b...@tufts.edu
www.tucf.org | genomics.med.tufts.edu
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