I am using freebayes in our local galaxy instance (v22.05). I used the option "Use stringent input base and mapping quality filters " which is supposed to set “–min-mapping-quality 30 --min-base-quality 20, --min-supporting-allele-qsum 0 --genotype-variant-threshold 0 (–standard-filters)”
Weirdly, the same options are also available to be set below this option again and checking the command and the vcf, sems like this radio button has no effect. Below is the image -
Please let me know also if I misunderstood or got the the options confused.
Interesting. Maybe there is some bug. Some tools are so complicated that the options are difficult to model in a GUI without some duplication. Certain combinations of options can also reveal corner-case conflicts.
Could you please produce a simple/small history at a public Galaxy server with that comparison? Either UseGalaxy.org or UseGalaxy.eu would be best for this. I’ll review first (or another moderator) then we can take that to the wrapper developers if needed. Post back the share link here.
With that information we can narrow down what is going on. Either improve the tool form or possibly add more help on it. Or fix the If you are interested in helping to model the solution that would be great … let’s sort out what is going wrong first. I don’t think what you are explaining is a known yet but could be wrong.
Dear Jennifer @jennaj ,
Thanks so much for looking into this. The history url for a small test on the EU website is Galaxy | Europe