## Mandatory ranking [unsupervised] # Weight value of prevalence to calculate weighted harmonic mean, named as beta parameter[ Default: 0.50 ] DNA_prevalence = 0.50 # Weight value of mean abundance to calculate weighted harmonic mean [ Default: 0.50 ] DNA_abundance = 0.50 [supervised] # Use the ecological property (abundance) to do prioritization. [required] required item, [optional] optional item, [none] ignoring. [ Default: required] DNA-within-phenotype_abundance = required # Use the ecological property (prevalence) to do prioritization. [required] required item, [optional] optional item, [none] ignoring. [ Default: required] DNA-within-phenotype_prevalence = required # Use the association with phenotypes (q values from associations) to do prioritization. [required] required item, [optional] optional item, [none] ignoring. [ Default: required] MaAsLin2_DA__qvalue = required # Use the association with phenotypes (effect size from associations) to do prioritization. [required] required item, [optional] optional item, [none] ignoring. [ Default: required] MaAsLin2_DA__mean(log) = required ## Binary filtering for selection subset # All [vignette_type] should be true # All [required] items should be true # At least one [optional] item should be true # All [none] items will be ignored # Default: select protein families significantly associated with the main clinical phenotype [filtering] # Filter for interested functional vignettes type [Choices: pilin | secreted_system | other user defined | none] vignettes = none # Filter for significant associations: [required] required item, [optional] optional item, [none] ignoring [ Default: required ] MaAsLin2_DA-sig = none # Filter for biochemical annotations: [required] required item, [optional] optional item, [none] ignoring ExpAtlas_interaction = optional DOMINE_interaction = optional SIFTS_interaction = optional Denovo_signaling = required Denovo_transmembrane = optional PSORTb_extracellular = optional PSORTb_cellWall = optional PSORTb_outerMembrane = optional UniRef90_extracellular = optional UniRef90_signaling = none UniRef90_transmembrane = optional UniRef90_cellWall = optional UniRef90_outerMembrane = optional UniRef90_PfamDomain = optional InterProScan_PfamDomain = optional InterProScan_SUPERFAMILY = optional InterProScan_ProSiteProfiles = optional InterProScan_ProSitePatterns = optional InterProScan_Gene3D = optional InterProScan_PANTHER = optional InterProScan_TIGRFAM = optional InterProScan_SFLD = optional InterProScan_ProDom = optional InterProScan_Hamap = optional InterProScan_SMART = optional InterProScan_CDD = optional InterProScan_PRINTS = optional InterProScan_PIRSF = optional InterProScan_MobiDBLite = optional