galaxyproject / galaxyproject/galaxy-visualizations

Support Qiime2 tools export nwk file format required.

Open
#132 5 comments 0 reactions 0 assignees View on GitHub
Dominant language
JavaScript
Stars
10
Forks
20
Avg merge
22h 17m
Merged PRs (30d)
14

Description

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 ](https://toolshed.g2.bx.psu.edu/repository?repository_id=4cb962eec018d64f) 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.

https://github.com/galaxyproject/galaxy-visualizations/blob/bad1e9cf14aa1ce540b12807db9bad82161898a8/packages/phylocanvas/public/phylocanvas.xml#L11

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

Contributor guide

No contributing guide indexed for this repository

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.