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@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
<softdev@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 <nate@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
>> > <softdev@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@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 <
>> > >> softdev@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
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>> >
>> > http://lists.bx.psu.edu/
>>
>
>
___________________________________________________________
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Kip Lord Bodi Jr.
Tufts University School of Medicine
136 Harrison Avenue, South Cove 502
Boston, MA 02118
617-636-3763
kip.bodi@tufts.edu
www.tucf.org | genomics.med.tufts.edu