On Thu, Feb 13, 2014 at 1:58 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote:
> Hi all,
> I just wanted to point out that there are several different ways to
> compare the history output item to a test file beyond the default
> "diff", including contains, re_match, sim_size, etc, this is set by
> the "compare" attribute in the xml tag for the test output.  If you
> really don't care about the contents of an output, you could, for
> example, use contains against an empty file.
> Sorry that I didn't provide more specific examples, as I am at
> a conference this week.

Thanks Dan - I don't think I'd seen the "contains" tag before,
and it isn't on the wiki yet:


Contains an empty file is a rather sneaky hack - I like it:

            <param name="job_type" value="genome" />
            <param name="job_quality" value="accurate" />
            <param name="type" value="none" />
            <param name="filenames" value="ecoli.fastq" ftype="fastqsanger" />
            <output name="out_fasta" file="ecoli.mira4_de_novo.fasta"
ftype="fasta" />
            <output name="out_bam" file="empty_file.dat" compare="contains" />
            <output name="out_maf" file="empty_file.dat" compare="contains" />
            <output name="out_log" file="empty_file.dat" compare="contains" />

It will do in the short term until the test framework supports
omitting some of the output test files... or I  could switch to
providing a snippet of data from each file.


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