Mercurial > repos > tomnl > mspurity_dimspredictpuritysingle

comparison combineAnnotations.R @ 12:d70fd233784a draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4f88143938cc198436c2691443832c87e2c31cd0
author tomnl
date Tue, 24 Sep 2019 08:07:38 -0400
parents a90832e6acb2
children 1389e565f95e
comparison
equal deleted inserted replaced
11:a90832e6acb2 12:d70fd233784a
65 # load in compound config 65 # load in compound config
66 # Soure local function taken from workflow4metabolomics 66 # Soure local function taken from workflow4metabolomics
67 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } 67 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
68 source_local("dbconfig.R") 68 source_local("dbconfig.R")
69 }else{ 69 }else{
70 compoundDbType = opt$compoundDbType 70 compoundDbType = compoundDbType
71 compoundDbName = NA 71 compoundDbName = NA
72 compoundDbHost = NA 72 compoundDbHost = NA
73 compoundDbPort = NA 73 compoundDbPort = NA
74 compoundDbUser = NA 74 compoundDbUser = NA
75 compoundDbPass = NA 75 compoundDbPass = NA
77 77
78 78
79 79
80 summary_output <- msPurity::combineAnnotations( 80 summary_output <- msPurity::combineAnnotations(
81 sm_resultPth = sm_resultPth, 81 sm_resultPth = sm_resultPth,
82 compoundDbPth = opt$compoundDbPth, 82 compoundDbPth = compoundDbPth,
83 metfrag_resultPth = opt$metfrag_resultPth, 83 metfrag_resultPth = opt$metfrag_resultPth,
84 sirius_csi_resultPth = opt$sirius_csi_resultPth, 84 sirius_csi_resultPth = opt$sirius_csi_resultPth,
85 probmetab_resultPth = opt$probmetab_resultPth, 85 probmetab_resultPth = opt$probmetab_resultPth,
86 ms1_lookup_resultPth = opt$ms1_lookup_resultPth, 86 ms1_lookup_resultPth = opt$ms1_lookup_resultPth,
87 ms1_lookup_keepAdducts = ms1_lookup_keepAdducts, 87 ms1_lookup_keepAdducts = ms1_lookup_keepAdducts,