Hi Geert, thanks for the bug report, I've fixed the bug upstream: https://github.com/bgruening/galaxytools/commit/cab6d1e84d440b7c73e99adc2bcb... Björn, can you release an update on the Tool Shed? I think we have accumulated a lot of fixes for GATK2 wrappers already. Nicola Il 2014-06-27 10:15 Geert Vandeweyer ha scritto:

Hi,

There is a missing parameter in the unified genotyer config from the iuc gatk2 wrapper: The following line should be added around line 204 (just before </expand></inputs>):

<param name="sample_ploidy" type="integer" value="2" label="Sample Ploidy (number of allles). For tumour, set to 2x the number of expected subclones" help="-ploidy,--sample_ploidy" />

Without this line, activating the advanced analysis options causes the job preparation to fail because there is a reference to it in the <command> section

gatk2 wrapper used: version : 8bcc13094767 hg tip: changeset: 3:2553f84b8174 tag: tip user: iuc date: Wed Feb 19 04:39:38 2014 -0500 summary: Uploaded

Best,

Geert

--

Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer

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