On Tue, Apr 19, 2011 at 2:23 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> What I need to work out now is how to use repeat parameters in the unit
> tests. There seems to be examples in tools/mutation/visualize.xml and
> tools/plotting/xy_plot.xml which only use the first repeat...

I've tried to skim all the provided tool XML files using <repeat> and
looked at their <test> entries. It looks like only a single repeat
parameter is being used in the tests currently.

The commented out <repeat> tags in tools/sr_assembly/velveth.xml
suggest repeat parameters don't work properly in <test> yet.

The comments in samtools/sam_merge.xml also suggest that (when
written), the test framework didn't handle <repeat> tags properly.

See also: https://bitbucket.org/galaxy/galaxy-central/issue/175/

Peter
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