Peter,

My recommendation would be to append or prepend the conditional name to each "use" parameter's name attribute, then specify the test parameters like:

<param name="useBackbone" value="false" />

There are good examples of how this is structured in tools/ngs_rna/cufflinks_wrapper.xml

--Dave B.

On 4/24/13 14:06:51.000, Peter Cock wrote:

Hi all,

I've not previously need to use a conditional parameter in a unit test, but for the MIRA wrapper this is essential. Here's my first attempt and the error when running the test:

https://bitbucket.org/peterjc/galaxy-central/commits/794ebc6cafecd3db9388f50...

 <tests>
     <test>
         <param name="job_method" value="denovo" />
         <param name="job_type" value="est" />
         <param name="job_qual" value="accurate" />
         <param name="condBackbone.use" value="false" />
         <param name="condSanger.use" value="true" />
         <param name="condSanger.filename" value="tvc_mini.fastq"

ftype="fastq" /> <param name="condRoche.use" value="false" /> <param name="condIllumina.use" value="false" /> <param name="condIonTorrent.use" value="false" /> <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />

</test> </tests>

Note that I can't refer to the parameters by the final part of their name ("use") as this is ambiguous. The dot syntax is natural to match that used in the Cheetah templates, but does not appear to work in the tool tests:

$ ./run_functional_tests.sh -id mira_assembler ... ====================================================================== ERROR: Assemble with MIRA v3.4 ( mira_assembler ) > Test-1

---

Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/mnt/galaxy/galaxy-central/test/functional/test_toolbox.py", line 76, in do_it page_inputs = self.__expand_grouping(testdef.tool.inputs_by_page[0], all_inputs) File "/mnt/galaxy/galaxy-central/test/functional/test_toolbox.py", line 118, in __expand_grouping if declared_inputs[ value.test_param.name ] == case.value: KeyError: 'use'

Is there something wrong with my test, or is this not yet supported?

Thanks,

Peter ___________________________________________________________ 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: http://lists.bx.psu.edu/

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