I am currently using galaxy main to run a filter pileup on datasets
that used the generate pileup tool. The filter pileup function is not
recognizing any of my generate pileup datasets in the drop-down box so
I cannot even execute the job. I think there may be a problem with
this tool. I would greatly appreciate any help or an update as to when
this tool will be functioning again.
My initial guess is that the datatype is not set as "pileup" for your
dataset - a standard, 6 column pileup format dataset. Perhaps you used
the option to generate a "consensus pileup" with 10 columns? And so
output is labeled as tabular format? If so, you can cut the first 3
columns and last 3 columns out, paste them together, and assign the
format "pileup" to use with the downstream filter tool. Tools to do
Cut/Paste are in the group 'Text Manipulation'.
If the datatype does not explain the issue, please let us know and we
can look into this more. From a quick test I didn't find anything
unusual, but of course we would want to track down any potential bugs,