clinicalmp-database-generation/main
v0.1

Workflow Type: Galaxy

The workflow begins with the Database Generation process. The Galaxy-P team has developed a workflow that collects protein sequences from known disease-causing microorganisms to build a comprehensive database. This extensive database is then refined into a smaller, more relevant dataset using the Metanovo tool.

Inputs

ID Name Description Type
Contaminants cRAP Protein Database #main/Contaminants cRAP Protein Database Contaminants cRAP Protein Database
  • File
Human SwissProt Protein Database #main/Human SwissProt Protein Database Human SwissProt Protein Database
  • File
Species UniProt Protein Database #main/Species UniProt Protein Database Species UniProt Protein Database
  • File
MS) datasets #main/Tandem Mass Spectrometry (MS/MS) datasets Tandem Mass Spectrometry (MS/MS) datasets
  • array containing
    • File

Steps

ID Name Description
4 Human UniProt Microbial Proteins cRAP for MetaNovo Merging FASTA files toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0
5 Metanovo Generating Customized Database toolshed.g2.bx.psu.edu/repos/galaxyp/metanovo/metanovo/1.9.4+galaxy4
6 Merge all FASTA Merge all FASTA toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0

Outputs

ID Name Description Type
Human UniProt Microbial Proteins cRAP for MetaNovo #main/Human UniProt Microbial Proteins cRAP for MetaNovo n/a
  • File
Human UniProt Microbial Proteins from MetaNovo cRAP #main/Human UniProt Microbial Proteins from MetaNovo cRAP n/a
  • File
Metanovo Compact CSV database #main/Metanovo Compact CSV database n/a
  • File
Metanovo Compact database #main/Metanovo Compact database n/a
  • File

Version History

v0.1 (earliest) Created 23rd Nov 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 db96f9c
help Creators and Submitter
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Additional credit

Subina Mehta

Submitter
Activity

Views: 150   Downloads: 37   Runs: 4

Created: 23rd Nov 2024 at 03:02

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