Hi All,
I am a bit lost here.
In my xml I have the following sections:
<inputs> <param type="data" format="tabular" name="amplitudes" label="amplitude file"/> <param name="samples" type="select" refresh_on_change="true" display="checkboxes" multiple="true" label="Mark quality control samples" dynamic_options='get_column_names(amplitudes)'/> </inputs>
<code file="dynamic_options.py" />
In my dynamic_options.py script, I want to parse the headers from 'amplitudes' file and show them in the checkboxes section.
My problem seems to be the following.
In python, amplitudes is a galaxy object: <galaxy.model.HistoryDatasetAssociation object at 0x7f4fc020a210>
How do I parse/access this file to get the headers?
It seems to be partly the same problem as asked last week in this conversation: http://dev.list.galaxyproject.org/Question-about-using-dynamic-options-and-r...
Thanks! Linda
Hi Linda,
I think your parameter definition will need to send the file_name of the HistoryDatasetAssociation, something like this...
<param name="samples" type="select" refresh_on_change="true" display="checkboxes" multiple="true" label="Mark quality control samples" dynamic_options='get_column_names(amplitudes.file_name)’/>
...and then your get_column_names() method should open the file to read the headers.
Let us know if this doesn’t work.
Greg Von Kuster
On Sep 22, 2015, at 7:45 AM, Linda Bakker linda.bakker@wur.nl wrote:
Hi All,
I am a bit lost here.
In my xml I have the following sections:
<inputs> <param type="data" format="tabular" name="amplitudes" label="amplitude file"/> <param name="samples" type="select" refresh_on_change="true" display="checkboxes" multiple="true" label="Mark quality control samples" dynamic_options='get_column_names(amplitudes)'/> </inputs>
<code file="dynamic_options.py" />
In my dynamic_options.py script, I want to parse the headers from 'amplitudes' file and show them in the checkboxes section.
My problem seems to be the following.
In python, amplitudes is a galaxy object: <galaxy.model.HistoryDatasetAssociation object at 0x7f4fc020a210>
How do I parse/access this file to get the headers?
It seems to be partly the same problem as asked last week in this conversation: http://dev.list.galaxyproject.org/Question-about-using-dynamic-options-and-r...
Thanks! Linda
-- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bakker@wur.nl
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Hi Greg, Wow that was easy! I was not expecting that. Thank you! Linda
On 09/22/2015 03:41 PM, Von Kuster, Greg wrote:
Hi Linda,
I think your parameter definition will need to send the file_name of the HistoryDatasetAssociation, something like this...
<param name="samples" type="select" refresh_on_change="true" display="checkboxes" multiple="true" label="Mark quality control samples" dynamic_options='get_column_names(amplitudes.file_name)’/>
...and then your get_column_names() method should open the file to read the headers.
Let us know if this doesn’t work.
Greg Von Kuster
On Sep 22, 2015, at 7:45 AM, Linda Bakker linda.bakker@wur.nl wrote:
Hi All,
I am a bit lost here.
In my xml I have the following sections:
<inputs> <param type="data" format="tabular" name="amplitudes" label="amplitude file"/> <param name="samples" type="select" refresh_on_change="true" display="checkboxes" multiple="true" label="Mark quality control samples" dynamic_options='get_column_names(amplitudes)'/> </inputs>
<code file="dynamic_options.py" />
In my dynamic_options.py script, I want to parse the headers from 'amplitudes' file and show them in the checkboxes section.
My problem seems to be the following.
In python, amplitudes is a galaxy object: <galaxy.model.HistoryDatasetAssociation object at 0x7f4fc020a210>
How do I parse/access this file to get the headers?
It seems to be partly the same problem as asked last week in this conversation: http://dev.list.galaxyproject.org/Question-about-using-dynamic-options-and-r...
Thanks! Linda
-- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bakker@wur.nl
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
galaxy-dev@lists.galaxyproject.org
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Von Kuster, Greg