Galaxy is not optimized for this kind of use case, I like to think of
it as sort of "file" centric - but it is clear more and more people
are using it to process data in this fashion. Hopefully someone chimes
in with better advice than I have :).
The way I would probably implement this is create a tool that lists
the available options out into a dataset or metadata of a dataset of a
new datatype - and then have your tool read that dataset in and build
the options using that file. Jim Johnson's mothur tools (available on
the tool shed) do a lot of this sort of thing - it may be worth
looking at the datatypes and an example such as remove.groups.xml:
...
<param name="group_in" type="data" format="groups" label="group - Groups"/>
<conditional name="groupnames">
<param name="source" type="select" label="Select Group Names from">
<option value="groups">A List of Group Names</option>
<option value="accnos">A History Group Name Accnos Dataset</option>
</param>
<when value="groups">
<param name="groups" type="select" label="groups - Pick groups to
remove" multiple="true">
<options>
<filter type="data_meta" ref="group_in" key="groups" />
</options>
</param>
</when>
<when value="accnos">
<param name="accnos" type="data" format="accnos" label="accnos -
Group Names from your history"/>
</when>
</conditional>
...
In particular the data_meta filter type in there.
-John
On Wed, Nov 6, 2013 at 8:03 AM, Biobix Galaxy <biobix.gal...@gmail.com> wrote:
> Hi all,
>
> We are working on a galaxy tool suite for data analysis.
> We use a sqlite db to keep result data centralised between the different
> tools.
>
> At one point the tool configuration options of a tool should be dependent on
> the rows within a table of the sqlite db that is the output of the previous
> step. In other words, we would like to be able to set selectable parameters
> based on an underlying sql statement. If sql is not possible, an alternative
> would be to output the table content into a txt file and subsequently parse
> the txt file instead of the sqlite_db within the xml configuration file.
>
> When looking through the galaxy wiki and mailing lists I came across the
> <code> tag which would be ideal, we could run a python script in the
> background to fetch date from the sqlite table, however that function is
> deprecated.
>
> Does anybody know of other ways to achieve this?
>
> Thanks!
>
> Jeroen
>
> Ir. Jeroen Crappé, PhD Student
> Lab of Bioinformatics and Computational Genomics (Biobix)
> FBW - Ghent University
>
>
>
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