No, I am not subclassing from Tabular. But when I do, it suddenly works. Thanks 
loads Dan!

cheers,
— 
Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden



On 07 Nov 2014, at 19:07, Daniel Blankenberg <d...@bx.psu.edu> wrote:

> Hi Jorrit,
> 
> Are you subclassing your tsv datatypes from tabular?
> 
> If you can post your tool xml and datatype_conf.xml additions then we should 
> be to provide more assistance.
> 
> 
> Thanks for using Galaxy,
> 
> Dan
> 
> 
> On Nov 7, 2014, at 12:27 PM, Jorrit Boekel <jorrit.boe...@scilifelab.se> 
> wrote:
> 
>> Dear list,
>> 
>> I tried to make a tool that takes tsv input and have some data_columns 
>> selection parameters in the xml definition. It seems to work, but I get 
>> ‘invalid option was selected’ in the browser interface for each of the 
>> data_columns. No logging errors or stacktraces. 
>> 
>> Digging a bit, I found out that the legal_values of the ColumnParameter (in 
>> lib/galaxy/tools/parameters/basic.py ) is empty. It is returned empty by 
>> get_column_list when this does 
>> if not dataset.metadata.columns: on line 1184 of the above mentioned file.
>> 
>> Now I’m a bit at a loss, how do I set these columns, or where are those 
>> columns set on the metadata? Is it stored, generated from the input file? My 
>> files are not official formats, just tsv subclasses.
>> 
>> 
>> I’m on changeset 14567:007f6a80629a in galaxy-dist. 
>> 
>> cheers,
>> — 
>> Jorrit Boekel
>> Proteomics systems developer
>> BILS / Lehtiö lab
>> Scilifelab Stockholm, Sweden
>> 
>> 
>> 
>> 
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