Am Donnerstag, den 13.02.2014, 14:23 +0000 schrieb Peter Cock:
On Thu, Feb 13, 2014 at 1:58 PM, Daniel Blankenberg <dan@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:
It's now added.
Contains an empty file is a rather sneaky hack - I like it:
<test> <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" /> </test>
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.
Thanks,
Peter