4 weeks ago by
If you are working at Galaxy Main (https://usegalaxy.org), the Plotting Tool is pending an update to be compatible with the functions mentioned in the GTN's metagenomics tutorial. Full details and progress on the update can be reviewed here: https://github.com/galaxyproject/usegalaxy-playbook/issues/71
The tool is already upgraded both in the Tool Shed (for use in a local/docker/cloud Galaxy) and at the Freiburg Public Galaxy server here: https://galaxy.uni-freiburg.de. I haven't run through the entire tutorial at the Freiburg server since the latest Galaxy release
17.09, but please ask questions if you run into anything else confusing in the tutorial or that you simply would like more help with - wherever you decide to work.
For the input selection, this is a dataset collection. This means that once you open the "Series" sections for the tool, hover over the icons for the input Dataset and click on the far right icon labeled "Dataset Collection" and you'll find the collapsed rarefaction dataset listed. You'll be opening multiple Series sections, choosing column1 as the X-axis and column2 for the Y-axis. Then opening another Series section and choosing column1 as the X-axis and column5 for the Y-axis. Repeat this for every 3rd column for the Y-axis section to produce the same graph as in the tutorial. I agree that this step could be made a bit more clear in the tutorial instructions and am following up on that.
GTN Tutorial for reference: http://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html
Thanks! Jen, Galaxy team