Re: [galaxy-dev] Proposed patch to blastxml_to_tabular.py
On Wed, Nov 30, 2011 at 9:49 AM, Peter van Heusden wrote:
Yes, this went away with newer versions of BLAST (and BLAST+). The 2.2.15 version is from 2006.
OK, that would explain why I didn't find the issue myself during the development.
I've added test data and tests to the tool's XML file.
Is this on a bitbucket fork?
Do you know how to run a single tool's test in Galaxy?
Peter
Yes, run_functional_tests.sh supports this. You'll need the test ID, which you can work out from the wrapper XML, or $ ./run_functional_tests.sh -list ... Then, in this case, $ ./run_functional_tests.sh -id blastxml_to_tabular ... Peter
On 30/11/2011 11:58, Peter Cock wrote:
On Wed, Nov 30, 2011 at 9:49 AM, Peter van Heusden wrote:
Yes, this went away with newer versions of BLAST (and BLAST+). The 2.2.15 version is from 2006. OK, that would explain why I didn't find the issue myself during the development.
I've added test data and tests to the tool's XML file. Is this on a bitbucket fork? Yes, its now at https://bitbucket.org/pvanheus/galaxy
I'm still trying to get my head around how to use mercurial, so things are no doubt messy. Look for changes from pvh@sanbi.ac.za
Do you know how to run a single tool's test in Galaxy?
Peter Yes, run_functional_tests.sh supports this. You'll need the test ID, which you can work out from the wrapper XML, or
$ ./run_functional_tests.sh -list ...
Then, in this case,
$ ./run_functional_tests.sh -id blastxml_to_tabular ... Ok doing that generates all sorts of stuff but ends with:
ok ---------------------------------------------------------------------- Ran 9 tests in 100.146s OK which sounds encouraging. Peter
Peter
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Peter van Heusden