Get .graphml support for galaxy cytoscape plugin

[hechth]

There is a visualization plugin for cytoscape files on GalaxyEU which would be useful for Galaxy - it should be able to read or visualize the graphml files if I am not mistaken. network.zip

[martenson]

Cytoscape is already available on umsa along with all other default viz, see https://umsa.cerit-sc.cz/visualizations

It can be run on .json and .sif files (the default for the tool), I don't think .eu has a different version with .graphml support.

[hechth]

Could it be extended to work with .graphml files?

[martenson]

I don't know enough about cytoscape or the formats in question -- I assume it can but would probably include implementing a parser. Maybe such tool exists?

The galaxy's plugin source is here: https://github.com/galaxyproject/galaxy/tree/dev/config/plugins/visualizations/cytoscape and the upstream at https://www.npmjs.com/package/cytoscape

[martenson]

https://github.com/iVis-at-Bilkent/cytoscape.js-graphml

[hechth]

Would it be possible to link this somehow with the existing galaxy tool? matchms.networking for example exports .graphml files which can be read by the cytoscape desktop app - this would be very useful if we want to create networks programmatically in python.

[martenson]

I am looking into it. Cytoscape needs a plugin for this to work and I am not sure that Galaxy's viz framework will support it, but I'll give it a shot.

[hechth]

Actually extending matchms networking with a .cyjs export is easier than this, which is already on the TODO list.

[martenson]

@hechth I spent some time on this issue but got nowhere yet, so this is good news. I'll pause my efforts here then.

[hechth]

I think this can be closed since https://github.com/matchms/matchms/pull/350 has been merged.