Mercurial > repos > computational-metabolomics > mspurity_averagefragspectra
comparison combineAnnotations.R @ 2:96fba93b4c8a draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 242de155f13acd6cb88946e89b5196ac55578aa8"
author | computational-metabolomics |
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date | Wed, 01 Apr 2020 11:05:00 -0400 |
parents | 50eedf5ad217 |
children | 52d48bcd3608 |
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1:4207233ead9c | 2:96fba93b4c8a |
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18 make_option("--metfrag_weight", type="numeric"), | 18 make_option("--metfrag_weight", type="numeric"), |
19 make_option("--sirius_csi_weight", type="numeric"), | 19 make_option("--sirius_csi_weight", type="numeric"), |
20 make_option("--probmetab_weight", type="numeric"), | 20 make_option("--probmetab_weight", type="numeric"), |
21 make_option("--ms1_lookup_weight", type="numeric"), | 21 make_option("--ms1_lookup_weight", type="numeric"), |
22 make_option("--biosim_weight", type="numeric"), | 22 make_option("--biosim_weight", type="numeric"), |
23 | 23 |
24 make_option("--summaryOutput", action="store_true"), | |
25 | |
24 make_option("--create_new_database", action="store_true"), | 26 make_option("--create_new_database", action="store_true"), |
25 make_option("--outdir", type="character", default="."), | 27 make_option("--outdir", type="character", default="."), |
26 | 28 |
27 make_option("--compoundDbType", type="character", default="sqlite"), | 29 make_option("--compoundDbType", type="character", default="sqlite"), |
28 make_option("--compoundDbPth", type="character", default=NA), | 30 make_option("--compoundDbPth", type="character", default=NA), |
54 'probmetab'=opt$probmetab_weight, | 56 'probmetab'=opt$probmetab_weight, |
55 'ms1_lookup'=opt$ms1_lookup_weight, | 57 'ms1_lookup'=opt$ms1_lookup_weight, |
56 'biosim'=opt$biosim_weight | 58 'biosim'=opt$biosim_weight |
57 ) | 59 ) |
58 print(weights) | 60 print(weights) |
61 | |
62 if (is.null(opt$probmetab_resultPth)){ | |
63 opt$probmetab_resultPth = NA | |
64 } | |
65 | |
59 if (round(!sum(unlist(weights),0)==1)){ | 66 if (round(!sum(unlist(weights),0)==1)){ |
67 stop(paste0('The weights should sum to 1 not ', sum(unlist(weights)))) | |
68 } | |
60 | 69 |
61 stop(paste0('The weights should sum to 1 not ', sum(unlist(weights)))) | 70 if (is.null(opt$summaryOutput)){ |
71 summaryOutput = FALSE | |
72 }else{ | |
73 summaryOutput = TRUE | |
62 } | 74 } |
63 | 75 |
64 if (opt$compoundDbType=='local_config'){ | 76 if (opt$compoundDbType=='local_config'){ |
65 # load in compound config | 77 # load in compound config |
66 # Soure local function taken from workflow4metabolomics | 78 # Soure local function taken from workflow4metabolomics |
74 compoundDbPort = NA | 86 compoundDbPort = NA |
75 compoundDbUser = NA | 87 compoundDbUser = NA |
76 compoundDbPass = NA | 88 compoundDbPass = NA |
77 } | 89 } |
78 | 90 |
79 | |
80 | |
81 summary_output <- msPurity::combineAnnotations( | 91 summary_output <- msPurity::combineAnnotations( |
82 sm_resultPth = sm_resultPth, | 92 sm_resultPth = sm_resultPth, |
83 compoundDbPth = compoundDbPth, | 93 compoundDbPth = compoundDbPth, |
84 metfrag_resultPth = opt$metfrag_resultPth, | 94 metfrag_resultPth = opt$metfrag_resultPth, |
85 sirius_csi_resultPth = opt$sirius_csi_resultPth, | 95 sirius_csi_resultPth = opt$sirius_csi_resultPth, |
92 compoundDbName = compoundDbName, | 102 compoundDbName = compoundDbName, |
93 compoundDbHost = compoundDbHost, | 103 compoundDbHost = compoundDbHost, |
94 compoundDbPort = compoundDbPort, | 104 compoundDbPort = compoundDbPort, |
95 compoundDbUser = compoundDbUser, | 105 compoundDbUser = compoundDbUser, |
96 compoundDbPass = compoundDbPass, | 106 compoundDbPass = compoundDbPass, |
97 weights = weights) | 107 weights = weights, |
108 summaryOutput = summaryOutput) | |
109 if (summaryOutput){ | |
110 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE) | |
111 } | |
112 | |
98 | 113 |
99 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE) | 114 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE) |
100 | 115 |
101 | 116 |
102 closeAllConnections() | 117 closeAllConnections() |