Grepping around the code I think this is the only way a ftype
attribute on an output affects the evaluation of test data.

                if attributes.get( 'ftype', None ) == 'bam':
                    local_fh, temp_name = self._bam_to_sam(
local_name, temp_name )
                    local_name = local_fh.name

I am not sure it was ever meant as a strict test.

I worry about breaking backward compatibility but it is easy enough to
implement this as an actual check when using newer API driven tests. I
have opened a pull request for this functionality here:

https://bitbucket.org/galaxy/galaxy-central/pull-request/347/check-ftype-attribute-if-defined-on-test/diff

Thoughts?

-John

On Tue, Mar 11, 2014 at 10:30 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Tue, Mar 11, 2014 at 2:58 PM, Björn Grüning
> <bjoern.gruen...@gmail.com> wrote:
>> Hi Peter,
>>
>> I think you need to have:
>>
>> <change_format>
>>        <when input="output.out_format" value="0" format="txt"/>
>>        <when input="output.out_format" value="0 -html" format="html"/>
>>        <when input="output.out_format" value="2" format="txt"/>
>>        <when input="output.out_format" value="2 -html" format="html"/>
>>        <when input="output.out_format" value="4" format="txt"/>
>>        <when input="output.out_format" value="4 -html" format="html"/>
>>        <when input="output.out_format" value="5" format="blastxml"/>
>> </change_format>
>>
>>
>> Sorry, can't test it right now.
>
> That seems to work - thanks Björn :)
>
> This seems to have exposed a bug in the <test> framework, e.g.
>
>         <test>
>             <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
>             <param name="db_opts_selector" value="file" />
>             <param name="subject" value="three_human_mRNA.fasta"
> ftype="fasta" />
>             <param name="database" value="" />
>             <param name="evalue_cutoff" value="1e-40" />
>             <param name="out_format" value="5" />
>             <param name="adv_opts_selector" value="basic" />
>             <output name="output1"
> file="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" />
>         </test>
>
> This was saying the output should have been "blastxml",
> but until I just fixed it the output was being tagged as
> "tabular" (although run_functional_tests.sh did check
> the content it didn't check the datatype matched).
>
> Dave - do think this is a reasonable enhancement?
>
> Peter
>
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