Hi Graham,
Instead of ${i.input.history_item_name}
Use "${i.input.name}"; I would also suggest using quotes around your argument
values that are being passed to the command line.
Thanks for using Galaxy,
Dan
On Nov 17, 2011, at 9:37 AM, graham etherington (TSL) wrote:
> Hi,
> I have a tool where the user selects their datasets from a drop-down list.
> The drop down list obviously contains the names of the suitable datasets
> as shown in the history and not that which is stored in the Galaxy
> database (e.g. ../database/files/011/dataset_11377.dat)
> I'm trying to access and pass the name of a history item to the command
> line parameters in the tool xml so I can use the dataset name as a
> column-header in an output file.
> Given the following fictitious xml snippet...
>
> <command interpreter="R">
> /home/galaxy/software/galaxy-central/tools/test_dir/test.R
> --args $ctl
> #for $i in $inputs
> ${i.input}
> #end for </command>
> <inputs>
> <repeat name="inputs" title="Input Files">
> <param name="input" type="data" format="txt" label="Dataset"/>
> </repeat>
> </inputs>
> <outputs>
> <data format="tabular" name="ctl" />
> </outputs>
>
> ...if the name of the history item selected in <parma name='input'> was
> "Dataset 1" how would I access that information, instead of only being
> able to access the name of the file in the Galaxy database (e.g.
> dataset_11377.dat)?
> I'm presuming I have to do something like:
> #for $i in $inputs
> ${i.input}
> ${i.input.history_item_name}
> #end for
>
> but I don't seem able to identify the correct syntax to get what I want.
> Any suggestions?
>
>
> Many thanks,
> Graham
>
>
> Dr. Graham Etherington
> Bioinformatics Support Officer,
> The Sainsbury Laboratory,
> Norwich Research Park,
> Norwich NR4 7UH.
> UK
> Tel: +44 (0)1603 450601
>
>
>
>
>
> On 17/11/2011 13:59, "Jeremy Goecks" <jeremy.goe...@emory.edu> wrote:
>
>> Nico,
>>
>> Does this happen when publishing new histories or just for histories that
>> have been published previously?
>>
>> If you're pulling from galaxy-central, you're running a very old version
>> of Galaxy. Currently tip is 6292:9b7d5c1c0be6 ; updating your instance to
>> tip may solve the problem as well.
>>
>> J.
>>
>> On Nov 17, 2011, at 8:00 AM, Nicolas Delhomme wrote:
>>
>>> Hi all,
>>>
>>> Since the last pull from galaxy-central (6056), whenever I try to
>>> access published histories, I get a file not found error; see the
>>> attached screenshot. I have not changed any configuration.
>>>
>>> Thanks for any pointers,
>>>
>>> Nico
>>>
>>> ---------------------------------------------------------------
>>> Nicolas Delhomme
>>>
>>> Genome Biology Computational Support
>>>
>>> European Molecular Biology Laboratory
>>>
>>> Tel: +49 6221 387 8310
>>> Email: nicolas.delho...@embl.de
>>> Meyerhofstrasse 1 - Postfach 10.2209
>>> 69102 Heidelberg, Germany
>>> ---------------------------------------------------------------
>>>
>>> <Screen shot 2011-11-17 at
>>> 13.56.18.png><ATT00001.txt>______________________________________________
>>> _____________
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>>
>>
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>
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