Hi Leandro,
Thanks! I had to change one line to get it working:
<command interpreter="perl"> ... #for $i in $add_inputs ${i.extra_table.file_name} #end for </command>
<repeat name="add_inputs" title="Extra Fitness Tables"> <param format="txt" name="extra_table" type="data" label="Another fitness table" /> </repeat>
Now galaxy will provide a list of files as the last parameters to the script.
Best,
Kip
On Fri, Jul 1, 2011 at 3:53 AM, Leandro Hermida softdev@leandrohermida.comwrote:
Hi Kip,
For the time being we are using this method to achieve the same result, although its not as nice as just having a multi-select menu in the form:
<command> ... $input1 #for $r in $add_inputs $r.$input2 #end for ... </command>
In <inputs>:
<param name="input1" type="data"/> <repeat name="add_inputs"> <param name="input2" type="data" /> </repeat>
best, Leandro
On Thu, Jun 30, 2011 at 4:52 PM, Kip Bodi kip.bodi@tufts.edu wrote:
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
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 > >>> > >>> > >> > >
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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