Tool XML form building bug with <options from_data_table="..."> ?
Has anyone run into this? I'm building a general-purpose filter control on my galaxy tool xml template for enabling numeric fields to be filtered by > < etc. parameters - in a user friendly way. I have a select list <para> driven by a data table: ... <param name="filter_column" type="select" label="Col"> <options from_data_table="bccdc_blast_fields" /> </param>...This works fine in building a list of fields to select from. Then I add <filter type="sort_by" column="1"/> <filter type="add_value" name="TESTESTTEST" value="WHWHWHW" /> but nothing happens, sort remains incorrect and no extra value. I try these same filters on a previous <param> in form that is driven by <options from_file="bccdc_blast_bins.loc"> and they work fine. I also tried applying <fiilter type="static_value" ...> to no avail on from_data_table options tag, but from from_file options, no problem. So I start to think there's a bug whereby NO filters work on <options from_data_table="bccdc_blast_fields" /> input? I've surveyed the galaxy.tools.parameters.dynamic_optionspython code, but can't see a decision point there in which from_data_table work vs from_file choice is made; is it in another script file? I'm using a BioLinux 2012 install that includes Galaxy. Help appreciated! Regards, Damion DooleyBC Centre for Disease ControlVancouver, BC
Moved to galaxy-dev, closing. Jen Galaxy team On 10/30/13 2:24 PM, damion@learningpoint.ca wrote:
Has anyone run into this? I'm building a general-purpose filter control on my galaxy tool xml template for enabling numeric fields to be filtered by > < etc. parameters - in a user friendly way. I have a select list <para> driven by a data table: ... <param name="filter_column" type="select" label="Col"> <options from_data_table="bccdc_blast_fields" /> </param> ... This works fine in building a list of fields to select from. Then I add <filter type="sort_by" column="1"/> <filter type="add_value" name="TESTESTTEST" value="WHWHWHW" />
but nothing happens, sort remains incorrect and no extra value. I try these same filters on a previous <param> in form that is driven by <options from_file="bccdc_blast_bins.loc"> and they work fine.
I also tried applying <fiilter type="static_value" ...> to no avail on from_data_table options tag, but from from_file options, no problem.
So I start to think there's a bug whereby NO filters work on <options from_data_table="bccdc_blast_fields" /> input? I've surveyed the galaxy.tools.parameters.dynamic_options python code, but can't see a decision point there in which from_data_table work vs from_file choice is made; is it in another script file?
I'm using a BioLinux 2012 install that includes Galaxy.
Help appreciated!
Regards,
Damion Dooley BC Centre for Disease Control Vancouver, BC
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Jennifer Jackson