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

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