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.

SEEK ID: https://workflowhub.eu/workflows/1216?version=1

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