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
<soft...@leandrohermida.com>wrote:

> 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.b...@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.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
> >
>



-- 
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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