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(a)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-an...
>
> 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(a)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/
--
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(a)wur.nl