Hello Galaxy folks

I'm building a tool to run the Trimmomatic program, and I've encountered an issue with filtering options from an external .loc file based on the value of a parameter which is defined within a conditional block.

The parameter definition looks like this:

    <conditional name="paired_end">
<param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" />
    <when value="no">

Subsequently I try to access the value of "is_paired_end" within a filter tag (to select a subset of items from a .loc file), using "ref_attribute" (based on the assumption that I'm trying to access "paired_end.is_paired_end"):

        <options from_file="adapters.loc">
<filter type="param_value" column="1" ref="paired_end" ref_attribute="is_paired_end" />

However this doesn't work, in that no options are returned by the filter. A debug statement in the relevant code for the ParamValueFilter (in dynamic_options.py) tells me that there's no "is_paired_end" attribute.

The only other tool I could find which uses "ref_attribute" is bfast_wrapper.xml, but this is accessing the "extension" attribute of a parameter not within a conditional (i.e. not the same as my example).

Should it be possible to do what I'm trying? Or is there a different way to do it?

Thanks for any help or suggestions,

Best wishes


Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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