Hi Pablo,
We recently installed 2.0.2 SnpEff at the UAB Galaxy instance (thanks for adding those mycoplasma genomes to SNPEff!) but we ran into some problems with the galaxy wrapper. It looks like it is for an older version of SnpEff and it chocks on the input options it is fed.
I replaced the input format section in snpEff.xml with:
<param name="inputFormat" type="select" label="Input format">
<option value=" -i txt ">Text</option>
<option value=" -i pileup ">Pileup</option>
<option value=" -i vcf ">VCF 4</option>
<option value=" -i bed ">BED</option>
</param>
It runs now, although I am sure there are other additional fixes that could be made to update the wrapper. Right now there is no option in the galaxy wrapper to output to VCF. If you could fix this that would be great, otherwise I can look into the format of the galaxy wrapper xml – something I need to do at eventually anyway.
-John