Tool XML form building bug with <options from_data_table="..."> ?
Moving this over to galaxy-dev@bx.psu.edu, the best list for tool design questions. Best! 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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
-- Jennifer Hillman-Jackson http://galaxyproject.org
Hey Damion, Because this wasn't explicitly shown in your example e-mail, can you verify for me that you are putting the filter elements inside of the options element and not inside of the param element? -John On Wed, Oct 30, 2013 at 10:50 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Moving this over to galaxy-dev@bx.psu.edu, the best list for tool design questions. Best! 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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
-- Jennifer Hillman-Jackson http://galaxyproject.org
___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
-
Jennifer Jackson -
John Chilton