Hi Geert,
thanks for the bug report, I've fixed the bug upstream:

https://github.com/bgruening/galaxytools/commit/cab6d1e84d440b7c73e99adc2bcb2c3c64c5b2c5

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.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer

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