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comparison combineAnnotations.R @ 15:70257c77ea04 draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
author tomnl
date Wed, 27 Nov 2019 12:34:20 +0000
parents c43861c6924b
children
comparison
equal deleted inserted replaced
14:998c58a7abb3 15:70257c77ea04
12 12
13 make_option("--ms1_lookup_checkAdducts", action="store_true"), 13 make_option("--ms1_lookup_checkAdducts", action="store_true"),
14 make_option("--ms1_lookup_keepAdducts", type="character", default=NA), 14 make_option("--ms1_lookup_keepAdducts", type="character", default=NA),
15 make_option("--ms1_lookup_dbSource", type="character", default="hmdb"), 15 make_option("--ms1_lookup_dbSource", type="character", default="hmdb"),
16 16
17 make_option(c("-sw","--sm_weight"),type="numeric"), 17 make_option("--sm_weight", type="numeric"),
18 make_option(c("-mw","--metfrag_weight"),type="numeric"), 18 make_option("--metfrag_weight", type="numeric"),
19 make_option(c("-cw","--sirius_csi_weight"),type="numeric"), 19 make_option("--sirius_csi_weight", type="numeric"),
20 make_option(c("-pw","--probmetab_weight"),type="numeric"), 20 make_option("--probmetab_weight", type="numeric"),
21 make_option(c("-lw","--ms1_lookup_weight"),type="numeric"), 21 make_option("--ms1_lookup_weight", type="numeric"),
22 make_option(c("-bw","--biosim_weight"),type="numeric"), 22 make_option("--biosim_weight", type="numeric"),
23 23
24 make_option("--create_new_database", action="store_true"), 24 make_option("--create_new_database", action="store_true"),
25 make_option(c("-o","--outdir"),type="character", default="."), 25 make_option("--outdir", type="character", default="."),
26 26
27 make_option("--compoundDbType", type="character", default="sqlite"), 27 make_option("--compoundDbType", type="character", default="sqlite"),
28 make_option("--compoundDbPth", type="character", default=NA), 28 make_option("--compoundDbPth", type="character", default=NA),
29 make_option("--compoundDbHost", type="character", default=NA) 29 make_option("--compoundDbHost", type="character", default=NA)
30 ) 30 )
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 = compoundDbType 70 compoundDbPth = opt$compoundDbPth
71 compoundDbType = opt$compoundDbType
71 compoundDbName = NA 72 compoundDbName = NA
72 compoundDbHost = NA 73 compoundDbHost = NA
73 compoundDbPort = NA 74 compoundDbPort = NA
74 compoundDbUser = NA 75 compoundDbUser = NA
75 compoundDbPass = NA 76 compoundDbPass = NA