Re: [galaxy-dev] parse history file/uploaded file with dynamic_options script

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&gt; 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/