matchms: Implement missing similarity metrics

hechth commented 3 years ago

Description

Implement matchms wrapper which exposes basic functionality of computing match scores between two msp files.

Subtasks

Galaxy

[x] Provide container/package to run as Galaxy tool
[x] Write wrapper script which handles IO
[x] Write tool script with tests
[x] Write documentation
[x] Implement choosing similarity metric
[x] Add option to mark as symmetric

Features

Implement missing similarity metrics which require special handling

[x] Modified cosine
[x] #278
[x] ParentmassMatch
[x] Fingerprint similarity
[x] #277
[x] #276
[x] #275

After the metadata match is implemented, this could also be used to provide a better implementation of the RI filtering by simply having it via the metadata match and then using a separate tool to combine scores.

martenson commented 3 years ago

initial version has been implemented in https://github.com/RECETOX/galaxytools/pull/55

hechth commented 1 year ago

parentmass match is implemented with the metadata match

hechth commented 1 year ago

This will be implemented with #321

RECETOX / galaxytools