search

RECETOX / galaxytools

Set of Galaxy tool wrappers developed at RECETOX
MIT License
13 stars 13 forks source link

Biotransformer: error from having mixtures as input #393

Open ElliottJP opened 1 year ago

ElliottJP commented 1 year ago

Biotransformer outputs misaligned - errors with e.g. random " additions. Galaxy history: https://umsa.cerit-sc.cz/u/elliott/h/columbiabootcamp2

xtrojak commented 1 year ago

@ElliottJP the actual error seems to be caused by incorrect input:

...
Working on compound: [Na+].[Na+].NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P](O)(=O)O[P](O)([O-])=O)[C@@H](O)[C@H]2O
ERROR: Input compound cannot be a mixture.
hechth commented 1 year ago

@ElliottJP seems like biotransformer would also require removing salts from the inputs?

hechth commented 10 months ago

This should be discussed with the package developers.

hechth commented 10 months ago

We agreed that this issue should be reported upstream and will not be fixed on this side with regard to havign mixtures in the list of SMILES. This will be solved separately.

We will investigate the output misalignment in this issue only and report the error upstream.

biotransformer_outputs.zip

hechth commented 10 months ago

xref for mixture filtering: https://github.com/RECETOX/galaxytools/issues/430