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@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 < 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
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
On Tue, May 24, 2011 at 1:31 PM, Leandro Hermida <softdev@leandrohermida.com> wrote: 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 >> >> >
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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
-- 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