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Hi @MEENU_GHAI
Correct, the qza and or qzv binary datatypes are not available in an uncompressed plain-text Galaxy “peek view” version. Just the metadata is exposed for now. This was likely on purpose, and I don’t know if it is possible to do something different. These tools were “wrapped” for Galaxy by the original authors, so asking them about future plans is where to start. I’m guessing that many people would find more ways to review these data useful!
I can let you know that the Galaxy implementation has some extra metadata that may be helpful. Think of this as another “level” to a QIMME2 datatype: similar to how a BED file can have 3 columns, or 4, or 6, or 12 and some tools will be picky about which is expects to work with.
WHERE to review QIIME2 data in Galaxy
Reviewing in these places can provide some context about why or why not a particular dataset (artifact) is available to a tool.
- Review the “Galaxy format dataype”. This is defined as qza for QIIME2 artifacts and qzv for QIIME2 visualizations.
- Next, click into the pencil-icon for any, and you’ll see a type of “sub-format” also defined for qza datasets.
- This is “detected” from the artifact content, can’t be modified directly by a user, and specifies what type of artifact you have.
- These types were defined by the QIIME2 authors – and should match what is expected when using the tools outside of Galaxy, too.
- How it works: Galaxy tool forms are performing a somewhat unique “double filter” when selecting an input dataset:
- the Galaxy format datatype needs to be qza or qzv
- and, the QIIME2 format needs to match what the tool is expecting
- then if both are true: a dataset in the history will be listed as potential input
HOW to review QIIME2 data in Galaxy
The current options to query, explore, and compute with qza and qzv compressed artifacts in Galaxy are the same as used on the command line. Meaning, these are the exact same tools, and have the same names and operations. The guides for usage are included in these places:
and the publication
- Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37(8), 852–857. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 | Nature Biotechnology
There isn’t a GTN Galaxy-specific tutorial (yet) but that may be developed in the future. 
If you have a more specific issue, you are still welcome to post more details. See the banner at this forum for how to get help with a tool error if that is what is going on. Thanks!
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As another option, you can download the .qza and .qzv files and view them with
https://view.qiime2.org/
This will let you view metadata, provenance, and the visualization within a .qzv file.
All Qiime2 artifacts are simply zip files, you can also extract them after downloading.
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Hi Jennifer,
Thanks.
This is what I see when I open a .qza file in galaxy. How can I go past this issue.
Kind regards
Meenu
Hi @MEENU_GHAI The file is compressed in Galaxy, and not in plain text.
To view it in plain text, you can try what @colinbrislawn is suggesting.
Thanks. As i am unable to use these .qza files in Galaxy, can i use.tsv metadata files to continue with alpha diversity and beta diversity analysis
Thanks Colin. i can view the .qzv files @ https://view.qiime2.org/ , however, i cannot use these files in galaxy to calculate alpha diversity, beta diversity etc of my samples
Okay! I’m glad you were able to open the files and see what’s inside!
Let’s see if we can get Galaxy working for you. Let’s start with these two questions:
Are you following a tutorial?
When you try to run an alpha diversity command, what does it show you?
I am not following a specific tutorial. The .qzv files are not accepted for alpha diversity analysis and the .qza do not seem to be in the right format.
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Hi Colin,
I have saved fastq files as fastq.gz and am exporting them into qiime2 artifact. I have few questions:
Try this tutorial: QIIME 2 Cancer Microbiome Intervention Tutorial — QIIME 2 Cancer Microbiome Intervention Tutorial
There are many small details that it covers. For example, .qzv files are visualizations and are not usually inputs… There should be .qza files you can upload for this step, as shown in the tutorial!