Support Qiime2 tools export nwk file format required.

[mthang]

Hi @guerler,
I am not certain if this is the right place to report this. This phylocanvas tree viewer only supports both newick and nhx file extension on Galaxy. The issue is that the Qiime2 tools export only produces tree with nwk as file format on galaxy, and the nwk can be detected as a valid file type on Galaxy. However, the phylocanvas only supports both newick and nhx as phylogenetic tree file. I wonder if phylocanvas could also support nwk file format on Galaxy. It is import to support nwk if Galaxy continues to support qiime2. Without nwk file format support, users need to change the file from nwk to nhx/newick manually.

galaxy-visualizations/packages/phylocanvas/public/phylocanvas.xml

Line 11 in bad1e9c

<model_class>HistoryDatasetAssociation</model_class>

This is an example of converting qza to newick with Qiiime2 on Galaxy

Example
Input : a qza file with Type ( Phylogeny[Unrooted])
tool : qiime2 tools export
setting :
The type of your input qza is : Phylogeney[Unrooted]
The current QIIME2 format is : NewickDirectoryFormat
To change the format, select the type indicated above:
Phylogency[Unrooted]
QIIME 2 file format to convert to:
Newick Format

thanks

[guerler]

Hi, can you share a screenshot? I only see newick as a valid type; nwk isn’t listed in the datatypes config.

[mthang]

This shows that qiime2 tools export produces nwk as the output file format in Galaxy and the phylogenetic tree viewer is not available after I clicked on the "visualize" button in the history.

The phylogenetic tree viewer is available to this after I changed the file type from nwk to either newick or nhx.

[guerler]

Thank you, I’ll look into this and add the datatype to the visualization if needed. Which Galaxy instance are you using?

[bgruening]

@mthang nwk is not a Galaxy datatype I think.

https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/datatypes_conf.xml.sample

I think we need to fix the tools.

[mthang]

@bgruening thank you for confirming that because I found this parser and it does not seem to support nwk datatype. Therefore, I am not sure which tool (phylogenetic tree viewer or qiime2 tool export) should I report to. https://github.com/galaxyproject/galaxy/blob/151aae36c493a893d85d66af334f00a0ab98c181/lib/galaxy/visualization/data_providers/phyloviz/__init__.py#L31