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
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.galaxy@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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Biobix Galaxy -
John Chilton