korseby
commented
4 years ago Hi @M123hx ,
First of all, you may want to have a look at regarding the reference of MetFrag-CLI: http://ipb-halle.github.io/MetFrag/projects/metfragcl/
With the CLI it is not possible to process more than one spectra at a time. The CLI already uses all available cores/threads and is very much optimized. However, you can use simple command line tools like parallel if you want to run more than one MetFrag-CLI at a time or use other tools to orchestrate several MEtFrag-CLI instances.
In the PhenoMeNal-project we developed a pipeline in Galaxy to run MetFrag in the cloud. Our colleagues have picked that project up. You may be interested in the following: https://github.com/computational-metabolomics/mspurity-galaxy
Older versions of that effort can be found here: https://github.com/phnmnl/container-metfrag-cli
and here: https://github.com/korseby/container-msnbase
We are also currently working on visualizing the results of the MetFrag-CLI.
hello, I want to use MetFrag CL to process multiple spectra with one call to MetFrag and in the end be able to tell in which spectrum the given compound was identified. Is there a way to do this, e.g. by writing mz and i values of multiple spectra to the peak list, or does MetFrag assume the peak list to be from only one spectrum?
could you tell me what a input multiple spectra paramater file format look like？ Best wishes!