A tool has to be created which takes outputs from RAMClustR (msp & csv) and matchms (scores, number of matches) and creates an output reporting in the mzTab format (https://pubmed.ncbi.nlm.nih.gov/30688441/).

Other tools around mzTab are https://github.com/lifs-tools/jmzTab-m and https://github.com/lifs-tools/pymzTab-m

Another possibility for reporting is via the MS-DIAL output format (example) which contains the intensities of the annotated features + the sample metadata.

Update 09.05.2024:

The tool should take 2 inputs:

• the Spec abundance table from the RAMClustR tool outputs
• the scores table from matchms formatter output.

The output should be the specAbundance table where some columns are renamed, depending on the inputs and parameters. The output should be a tabular file

We need a single select which states whether to use single or multiple annotation.

If single is selected, then if there are multiple rows having the same query, choose the reference with the maximum score.

If multiple is allowed, concatenate all reference identifiers separated by , and use the concatenated string as the column header.