allows an optional input --i-ms2-matches of type FeatureData[Molecules] in make-hierarchy. This is a table that contains MS/MS spectral matches for features. Must contain the column Smiles
updates get-classyfire-taxonomy such that the input --i-feature-data must contain the columns csi_smiles and ms2_smiles (as opposed to just smiles before). Classyfire is run on ms2_smiles whenever available. Otherwise, it is run on csi_smiles
updates _itol_metadata.py such that the output --color-file-path has dashed clades when csi_smiles are used for Classyfire taxonomy assignment.
updates documentation to instruct users on the usage of the new features
This PR:
--i-ms2-matches
of type FeatureData[Molecules] in make-hierarchy. This is a table that contains MS/MS spectral matches for features. Must contain the columnSmiles
--i-feature-data
must contain the columnscsi_smiles
andms2_smiles
(as opposed to justsmiles
before). Classyfire is run onms2_smiles
whenever available. Otherwise, it is run oncsi_smiles
_itol_metadata.py
such that the output--color-file-path
has dashed clades whencsi_smiles
are used for Classyfire taxonomy assignment.