Is there a tool on Galaxy that will calculate alpha and beta diversity from Metaphlan relative abundance tables? Rather than using the command line utility scripts? Thanks!
Hi @bethp
These two are probably what you are looking for. They can accept a biom file, which you have or can get from Metaphlan data, yes?
Search the tool panel with alpha and beta to find these and more:
- Calculate alpha diversity
- Calculate beta diversity
The others use a Kraken file or are part of Mother or Phyloseq. So, you have a few options. And if you do want to go into the command line, maybe a Jupyter notebook is an easy way to move between your history and that sort of environment for custom queries that you can save somewhere for reuse.
Hope this helps!
This is what I am seeing when i search alpha, and they are not accepting biom files - were there specific tools you were thinking of? Thanks!
Hi @bethp
Are you searching at the UseGalaxy.org server? I see the same results there.
Try instead at the UseGalaxy.eu server for now. Screenshot.
The Micro-Galaxy researchers are working on new workflows at the EU server as baseline. This involves wrapping more tools and updating others. This work will eventually flow out to the GTN and all of the other UseGalaxy servers.
This tool is from the Qiime package but it was changed a bit to work with other files types (instead of the qza artifacts). Or that is at least how I understand it, and the Qiime2 version is everywhere but this breakout is not yet.
I’ll follow up about getting these specific tools installed at ORG but please do not wait, ok? There might be a “delay” reason I don’t know about yet. It is very easy to move data between servers – per file or entire histories.
Please give that a try!
The microbime researchers might have more ideas. I’m going to ask them for feedback next.
Update: request tracking ticket for ORG
Thanks @jennaj - i’ll try out the EU versions of the tools that don’t require qza. I’m also looking for a PERMANOVA tool but I think this currently is also only through qiime?
Hi @bethp – Glad that will work for you and from what I can find out, I think you are right about the other analysis variation – it was introduced in the Qimme2 package and all of those work with the qza artifacts.
You can create the artifacts in Galaxy but refer to the original docs for how to get those organized correctly (especially the sample sheets aka “metadata” files). More “how to in Galaxy” is pending for that suite, and the create tool itself will probably update, along with an automatic link out to the artifact inspector. For now you can download the qza/qzv from Galaxy then use their website.
This prior topic has the most details all in a summary, including feedback from the tool author himself! → unable to use .qza files
If you run into a specific usage problem not covered in the tool docs we can try to ping them with your new questions, too, if I am unsure about how to solve it.