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:
<param name="is_paired_end" type="boolean" label="Paired end data?"
truevalue="yes" falsevalue="no" checked="on" />
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
<filter type="param_value" column="1" ref="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,
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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