In my browser window, Varscan for variant detection does not allow me to add datasets. What is wrong/what am I doing wrong?
See below. This is how the tool looks.
Thanks!
Anand
Tool name: Varscan
Tool version: 0.1
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/varscan_version_2/varscan/0.1
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/varscan_version_2
Hello,
Is the datatype "pileup" assigned to your dataset? If not, assign and try again. Here is how:
http://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset
Thanks, Jen, Galaxy team
Moin,
Varscan is taking a "pileup" file as input and you probably don't have any pileup file in your history. Please generate at first such a file, for example with the samtools suite.
Ciao,
Bjoern
Good advice! I just want to add that 'pileup' is not assigned by default with the SAM Pileup/Mpileup tools. Those results need the metadata 'datatype' change. I am not going to open a ticket for this, as it is a known, and new changes to tools are underway. Should the new versions also have this issue, I will put it in as an enhancement request. Thanks! Jen. Galaxy team.
Thanks guys. I'll check my workflow again.
One last comment, if running the pileup tool in a workflow, you can include the metadata 'datatype' assignment using the "Edit Step Actions -> Change Datatype" function (far right panel in the editor). Select the tool, then review and add in this function. Thanks, Jen, Galaxy team