Metabolome Annotation Workflow (MAW)
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Download RO CrateMetabolome Annotation Workflow (MAW) takes liquid chromatography tandem mass spectrometry data (LC-MS2) as .mzML format data files. It performs spectral database dereplication using R Package Spectra and compound database dereplication using MetFrag/SIRIUS. Final candidate selection is executed in Python using RDKit and PubChemPy. The classification of the tentative candidates from the input data are classified using ChemONT chemical ontology.
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Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| python_script | n/a | n/a |
|
| r_script | n/a | n/a |
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| mzml_files | n/a | n/a |
|
| gnps_file | n/a | n/a |
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| hmdb_file | n/a | n/a |
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| mbank_file | n/a | n/a |
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| file_id | n/a | n/a |
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| ppmx | n/a | n/a |
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| collision_info | n/a | n/a |
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| db_name | n/a | n/a |
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| db_path | n/a | n/a |
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Steps
| ID | Name | Description |
|---|---|---|
| analysis | n/a | n/a |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| candidate_files | n/a | n/a |
|
| result | n/a | n/a |
|
Version History
main @ 2da7fba (latest) Created 1st Aug 2023 at 15:21 by Mahnoor Zulfiqar
updated with all versions information
Frozen
main2da7fba
main @ 1be2bd3 (earliest) Created 19th Jun 2023 at 21:09 by Mahnoor Zulfiqar
use docker to run MAW
Frozen
main
1be2bd3
Creators and Submitter
Views: 1492
Created: 19th Jun 2023 at 21:09
Last updated: 1st Aug 2023 at 15:21
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https://orcid.org/0000-0002-2961-9670
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In the age of high-throughput data, computational workflows have made data processing tasks flexible, manageable, and automated. To administer different computational activities in a workflow, different workflow management systems (WMS) are used that necessitate a sophisticated level of standardisation. Standardisation and reproducibility can be achieved by using standard formats for specifying workflows, such as Common Workflow Language (CWL), and provenance gathering with the standard W3C PROV ...
Creator: Mahnoor Zulfiqar
Submitter: Mahnoor Zulfiqar
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