Question: Snpeff 2.0.2 Wrapper Problem / Partial Fix
0
John David Osborne • 160 wrote:
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