Workflow Type: Common Workflow Language
Stable

This repository hosts Metabolome Annotation Workflow (MAW). The workflow takes MS2 .mzML format data files as an input in R. It performs spectral database dereplication using R Package Spectra and compound database dereplication using SIRIUS OR MetFrag . Final candidate selection is done in Python using RDKit and PubChemPy.

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Inputs

ID Name Description Type
python_script n/a n/a
  • File
r_script n/a n/a
  • File
mzml_files n/a n/a
  • File[]
gnps_file n/a n/a
  • File
hmdb_file n/a n/a
  • File
mbank_file n/a n/a
  • File
ppmx n/a n/a
  • int
collision_info n/a n/a
  • boolean
db_name n/a n/a
  • string
db_path n/a n/a
  • File

Steps

ID Name Description
analysis n/a n/a

Outputs

ID Name Description Type
candidate_files n/a n/a
  • array containing
    • array containing
      • File
result n/a n/a
  • File[]

Version History

main @ 2da7fba (latest) Created 1st Aug 2023 at 15:21 by Mahnoor Zulfiqar

updated with all versions information


Frozen main 2da7fba

main @ 1be2bd3 (earliest) Created 19th Jun 2023 at 21:09 by Mahnoor Zulfiqar

use docker to run MAW


Frozen main 1be2bd3
help Creators and Submitter
Creators
Submitter
Citation
Zulfiqar, M., Crusoe, M. R., Gadelha, L., Steinbeck, C., Sorokina, M., & Peters, K. (2023). Metabolome Annotation Workflow (MAW). WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.510.2
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Views: 1352

Created: 19th Jun 2023 at 21:09

Last updated: 1st Aug 2023 at 15:21

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Total size: 8.31 MB
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