lcmsmatching: search-mz annotate

annotate search-mz @ 5:18254e8d1b72 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb-dirty

author	prog
date	Thu, 16 Mar 2017 08:15:11 -0400
parents	1ba222315fd5
children	b8f70d8216b3

rev	line source
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	1 #!/usr/bin/env Rscript
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	2 # vi: ft=R
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	3 args <- commandArgs(trailingOnly = F)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	4 script.path <- sub("--file=","",args[grep("--file=",args)])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	5 library(getopt)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	6 source(file.path(dirname(script.path), 'msdb-common.R'), chdir = TRUE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	7 source(file.path(dirname(script.path), 'MsFileDb.R'), chdir = TRUE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	8 source(file.path(dirname(script.path), 'MsPeakForestDb.R'), chdir = TRUE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	9 source(file.path(dirname(script.path), 'MsXlsDb.R'), chdir = TRUE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	10 source(file.path(dirname(script.path), 'Ms4TabSqlDb.R'), chdir = TRUE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	11 source(file.path(dirname(script.path), 'MsDbLogger.R'), chdir = TRUE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	12 source(file.path(dirname(script.path), 'MsDbInputDataFrameStream.R'), chdir = TRUE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	13 source(file.path(dirname(script.path), 'MsDbOutputDataFrameStream.R'), chdir = TRUE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	14 source(file.path(dirname(script.path), 'htmlhlp.R'), chdir = TRUE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	15 source(file.path(dirname(script.path), 'strhlp.R'), chdir = TRUE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	16 source(file.path(dirname(script.path), 'fshlp.R'), chdir = TRUE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	17 source(file.path(dirname(script.path), 'biodb-common.R'), chdir = TRUE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	18 source(file.path(dirname(script.path), 'nethlp.R'), chdir = TRUE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	19
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	20 # Missing paste0() function in R 2.14.1
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	21 if (as.integer(R.Version()$major) == 2 && as.numeric(R.Version()$minor) < 15)
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	22 paste0 <- function(...) paste(..., sep = '')
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	23
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	24 #############
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	25 # CONSTANTS #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	26 #############
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	27
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	28 PROG <- sub('^.*/([^/]+)$', '\\1', commandArgs()[4], perl = TRUE)
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	29 USERAGENT <- 'search-mz ; pierrick.roger@gmail.com'
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	30
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	31 # Authorized database types
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	32 MSDB.XLS <- 'xls'
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	33 MSDB.4TABSQL <- '4tabsql'
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	34 MSDB.FILE <- 'file'
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	35 MSDB.PEAKFOREST <- 'peakforest'
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	36 MSDB.VALS <- c(MSDB.XLS, MSDB.4TABSQL, MSDB.FILE, MSDB.PEAKFOREST)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	37
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	38 # Authorized mode values
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	39 POS_MODE <- 'pos'
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	40 NEG_MODE <- 'neg'
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	41 MSDB.MODE.VALS <- c(POS_MODE, NEG_MODE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	42
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	43 # Default
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	44 MSDB.DFT <- list()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	45 MSDB.DFT[['mzshift']] <- 0 # in ppm
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	46 MSDB.DFT[['mzprec']] <- 5 # in ppm
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	47 MSDB.DFT[['mztolunit']] <- MSDB.DFT.MZTOLUNIT
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	48 MSDB.DFT[['precursor-rt-tol']] <- 5
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	49 MSDB.DFT[['molids-sep']] <- MSDB.DFT.MATCH.SEP
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	50 MSDB.DFT[['db-fields']] <- concat.kv.list(msdb.get.dft.db.fields())
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	51 MSDB.DFT[['db-ms-modes']] <- concat.kv.list(MSDB.DFT.MODES)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	52 MSDB.DFT[['pos-prec']] <- paste(MSDB.DFT.PREC[[MSDB.TAG.POS]], collapse = ',')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	53 MSDB.DFT[['neg-prec']] <- paste(MSDB.DFT.PREC[[MSDB.TAG.NEG]], collapse = ',')
4 1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	54 MSDB.DFT[['db-rt-unit']] <- MSDB.RTUNIT.SEC
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	55 MSDB.DFT[['rtunit']] <- MSDB.RTUNIT.SEC
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	56 DEFAULT.ARG.VALUES <- MSDB.DFT
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	57 DEFAULT.ARG.VALUES[['input-col-names']] <- concat.kv.list(msdb.get.dft.input.fields())
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	58 DEFAULT.ARG.VALUES[['output-col-names']] <- concat.kv.list(msdb.get.dft.output.fields())
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	59
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	60 ##############
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	61 # PRINT HELP #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	62 ##############
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	63
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	64 print.help <- function(spec, status = 0) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	65 cat(getopt(spec, usage = TRUE, command = PROG))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	66 q(status = status)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	67 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	68
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	69 ###############################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	70 # SET DEFAULT ARGUMENT VALUES #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	71 ###############################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	72
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	73 set.dft.arg.val <-function(opt) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	74
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	75 for (f in names(MSDB.DFT))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	76 if (is.null(opt[[f]]))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	77 opt[[f]] <- MSDB.DFT[[f]]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	78
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	79 # Set default values
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	80 if ( opt$database == MSDB.XLS && ! is.null(opt$url) && is.null(opt[['cache-dir']]))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	81 opt[['cache-dir']] <- file.path(opt$url, 'cache')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	82
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	83 if ( ! is.null(opt$rtcol) && opt$rtcol == '')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	84 opt$rtcol <- NULL
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	85
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	86 return(opt)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	87 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	88
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	89 #########################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	90 # PARSE ARGUMENT VALUES #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	91 #########################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	92
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	93 parse.arg.val <- function(opt) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	94
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	95 # Parse input column names
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	96 if ( ! is.null(opt[['db-fields']])) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	97 cust <- split.kv.list(opt[['db-fields']])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	98 opt[['db-fields']] <- split.kv.list(MSDB.DFT[['db-fields']])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	99 opt[['db-fields']][names(cust)] <- cust
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	100 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	101
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	102 # Parse MS modes
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	103 if ( ! is.null(opt[['db-ms-modes']])) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	104 cust <- split.kv.list(opt[['db-ms-modes']])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	105 opt[['db-ms-modes']] <- split.kv.list(MSDB.DFT[['db-ms-modes']])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	106 opt[['db-ms-modes']][names(cust)] <- cust
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	107 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	108
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	109 # Parse retention time columns
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	110 if ( ! is.null(opt$rtcol))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	111 opt$rtcol <- strsplit(opt$rtcol, ',')[[1]]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	112
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	113 # Parse input column names
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	114 if (is.null(opt[['input-col-names']])) {
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	115 opt[['input-col-names']] <- msdb.get.dft.input.fields()
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	116 }
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	117 else {
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	118 custcols <- split.kv.list(opt[['input-col-names']])
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	119 dftcols <- msdb.get.dft.input.fields()
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	120 opt[['input-col-names']] <- c(custcols, dftcols[ ! names(dftcols) %in% names(custcols)])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	121 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	122
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	123 # Parse output column names
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	124 if (is.null(opt[['output-col-names']])) {
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	125 # By default keep input col names for output
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	126 opt[['output-col-names']] <- msdb.get.dft.output.fields()
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	127 input.cols <- names(opt[['input-col-names']])
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	128 output.cols <- names(opt[['output-col-names']])
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	129 opt[['output-col-names']] <- c(opt[['input-col-names']][input.cols %in% output.cols], opt[['output-col-names']][ ! output.cols %in% input.cols])
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	130 }
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	131 else {
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	132 custcols <- split.kv.list(opt[['output-col-names']])
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	133 dftcols <- msdb.get.dft.output.fields()
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	134 opt[['output-col-names']] <- c(custcols, dftcols[ ! names(dftcols) %in% names(custcols)])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	135 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	136
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	137 # Parse lists of precursors
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	138 if ( ! is.null(opt[['pos-prec']]))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	139 opt[['pos-prec']] <- split.str(opt[['pos-prec']], unlist = TRUE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	140 if ( ! is.null(opt[['neg-prec']]))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	141 opt[['neg-prec']] <- split.str(opt[['neg-prec']], unlist = TRUE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	142
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	143 return(opt)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	144 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	145
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	146 #################################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	147 # PRINT DEFAULT ARGUMENT VALUES #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	148 #################################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	149
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	150 print.dft.arg.val <- function(opt) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	151
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	152 print.flags <- DEFAULT.ARG.VALUES
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	153 names(print.flags) <- vapply(names(print.flags), function(x) paste0('print-', x), FUN.VALUE = '')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	154 for (f in names(print.flags))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	155 if ( ! is.null(opt[[f]])) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	156 cat(print.flags[[f]])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	157 q(status = 0)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	158 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	159 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	160
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	161 make.getopt.spec.print.dft <- function() {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	162
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	163 spec <- character()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	164
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	165 for (f in names(DEFAULT.ARG.VALUES))
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	166 spec <- c(spec, paste0('print-', f), NA_character_, 0, 'logical', paste0('Print default value of --', f))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	167
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	168 return(spec)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	169 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	170
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	171 ##############################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	172 # MAKE GETOPT SPECIFICATIONS #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	173 ##############################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	174
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	175 make.getopt.spec <- function() {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	176 spec = c(
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	177 'help', 'h', 0, 'logical', 'Print this help.',
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	178 'mode', 'm', 1, 'character', paste0('MS mode. Possible values are:', paste(MSDB.MODE.VALS, collapse = ", "), '.'),
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	179 'mzshift', 's', 1, 'numeric', paste0('Shift on m/z, in ppm. Default is ', MSDB.DFT$mzshift,'.'),
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	180 'mzprec', 'p', 1, 'numeric', paste0('Tolerance on m/z, in ppm. Default is ', MSDB.DFT$mzprec,'.'),
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	181 'mztolunit', NA_character_, 1, 'character', paste0('Tolerance on m/z, in ppm. Default is ', MSDB.DFT$mztolunit,'.'),
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	182 'rttol', 'r', 1, 'numeric', paste0('Tolerance on retention times. Unset by default.'),
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	183 'rttolx', 'x', 1, 'numeric', paste0('Tolerance on retention times. Unset by default.'),
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	184 'rttoly', 'y', 1, 'numeric', paste0('Tolerance on retention times. Unset by default.'),
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	185 'rtcol', 'c', 1, 'character', paste0('Chromatographic column to use. Unset by default. If set, use the corresponding column to filter on retention times, if retention times are provided.'),
4 1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	186 'rtunit', NA_character_, 1, 'character', paste0('Retention time unit for the input file. Default is ', MSDB.DFT$rtunit, '. Allowed values are:', paste(MSDB.RTUNIT.VALS, collapse = ", "), '.'),
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	187 'all-cols', NA_character_, 0, 'logical', 'Use all available chromatographic columns to match retention times.',
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	188 'check-cols', NA_character_, 0, 'logical', 'Check that the chromatographic column names specified with option -c really exist.',
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	189 'list-cols', NA_character_, 0, 'logical', 'List all chromatographic columns present in the database. Write list inside the file specified by -o option.',
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	190 'same-rows', 'a', 0, 'logical', 'If set, output exactly the same number of rows as the input. This means that in case of multiple matches for one mz, then only one line is output (i.e.: the mz value is not duplicated on several lines). In the main output file, an "ms.matching" column is output with inside, for each mz, a comma separated list of matched component/molecule IDs. If unset, then only the main output file is used, and one single is written to it with one line per peak match, and eventual mz line duplicated if there are multiple matches for this mz.',
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	191 'same-cols', 'b', 0, 'logical', 'If set, output the same columns as inside the input. All input columns are copied to the output.',
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	192 'input-file', 'i', 1, 'character', 'Set input file.',
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	193 'output-file', 'o', 1, 'character', 'Set file to use for the main output.',
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	194 'peak-output-file', NA_character_, 1, 'character', 'If set and if --same-rows is set, then output all matches inside the specified file, with one mz match per line. The output columns are: mz, rt, id, col, colrt, composition, attribution. This means that if an mz value is matched several times, then it will repeated on several lines, with one match description per line.',
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	195 'html-output-file', NA_character_, 1, 'character', 'Set file to use for the HTML output.',
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	196 'no-main-table-in-html-output', NA_character_, 0, 'logical', 'Do not display main table in HTML output.',
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	197 'precursor-match', NA_character_, 0, 'logical', 'Remove peaks whose molecule precursor peak has not been matched. Unset by default.',
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	198 'precursor-rt-tol', NA_character_, 1, 'numeric', paste0('Precursor retention time tolerance. Only used when precursor-match is enabled. Default is ', MSDB.DFT[['precursor-rt-tol']], '.'),
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	199 'pos-prec', NA_character_, 1, 'character', paste0('Set the list of precursors to use in positive mode. Default is "', MSDB.DFT[['pos-prec']], '".'),
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	200 'neg-prec', NA_character_, 1, 'character', paste0('Set the list of precursors to use in negative mode. Default is "', MSDB.DFT[['neg-prec']], '".'),
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	201 'input-col-names', NA_character_, 1, 'character', paste0('Set the input column names. Default is "', DEFAULT.ARG.VALUES[['input-col-names']], '".'),
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	202 'output-col-names', NA_character_, 1, 'character', paste0('Set the output column names. Default is "', DEFAULT.ARG.VALUES[['output-col-names']], '".'),
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	203 'molids-sep', NA_character_, 1, 'character', paste0('Set character separator used to when concatenating molecule IDs in output. Default is "', MSDB.DFT[['molids-sep']] , '".'),
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	204 'first-val', NA_character_, 0, 'logical', 'Keep only the first value in multi-value fields. Unset by default.',
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	205 'excel2011comp', NA_character_, 0, 'logical', 'Excel 2011 compatiblity mode. Output ASCII text files instead of UTF-8 files, where greek letters are replaced with their latin names, plusminus sign is replaced with +- and apostrophe is replaced with \"prime\". All other non-ASCII characters are repladed with underscore.',
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	206 'database', 'd', 1, 'character', paste0('Set database to use: "xls" for an Excel database, "file" for a single file database, "4tabsql" for a 4Tab SQL database, and "peakforest" for a connection to PeakForest database.'),
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	207 'url', NA_character_, 1, 'character', 'URL of database. For "peakforest" database it is the HTTP URL, for the "xls" database it is the path to the directory containing the Excel files, for the "file" database it is the path to the file database and for the "4tabsql" database it is the IP address of the server.',
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	208 'cache-dir', NA_character_, 1, 'character', 'Path to directory where to store cache files. Only used when database flag is set to "xls".',
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	209 'db-name', NA_character_, 1, 'character', 'Name of the database. Used by the "4tabsql" database.',
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	210 'db-user', NA_character_, 1, 'character', 'User of the database. Used by the "4tabsql" database.',
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	211 'db-password', NA_character_, 1, 'character', 'Password of the database user. Used by the "4tabsql" database.',
4 1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	212 'db-fields', NA_character_, 1, 'character', paste0('Comma separated key/value list giving the field names to be used in the single file database. Default is "', MSDB.DFT[['db-fields']], '".'),
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	213 'db-ms-modes', NA_character_, 1, 'character', paste0('Comma separated key/value list giving the MS modes to be used in the single file database. Default is "', MSDB.DFT[['db-ms-modes']], '".'),
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	214 'db-rt-unit', NA_character_, 1, 'character', paste0('Retention time unit for the database, used in the single file database. Default is "', MSDB.DFT[['db-rt-unit']], '". Allowed values are:', paste(MSDB.RTUNIT.VALS, collapse = ", "), '.'),
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	215 'db-token', NA_character_, 1, 'character', 'Database token. Used by Peakforest database.',
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	216 'debug', NA_character_, 0, 'logical', 'Set debug mode.'
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	217 )
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	218
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	219 spec <- c(spec, make.getopt.spec.print.dft())
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	220
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	221 if ( ! is.null(spec))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	222 spec <- matrix(spec, byrow = TRUE, ncol = 5)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	223
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	224 return(spec)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	225 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	226
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	227 #############
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	228 # READ ARGS #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	229 #############
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	230
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	231 read_args <- function() {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	232
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	233 # options
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	234 spec <- make.getopt.spec()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	235 opt <- getopt(spec)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	236
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	237 # help
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	238 if ( ! is.null(opt$help))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	239 print.help(spec)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	240
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	241 print.dft.arg.val(opt) # Print default values
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	242 opt <- set.dft.arg.val(opt) # Set default values
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	243 opt <- parse.arg.val(opt) # Parse list values
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	244
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	245 # Check values
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	246 error <- .check.db.conn.opts(opt)
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	247 if (is.null(opt[['output-file']]) && is.null(opt[['list-cols']])) {
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	248 warning("You must set a path for the output file.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	249 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	250 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	251 if (is.null(opt[['list-cols']])) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	252 if (is.null(opt[['input-file']])) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	253 warning("You must provide an input file.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	254 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	255 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	256 if (is.null(opt$mode) \|\| ( ! opt$mode %in% MSDB.MODE.VALS)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	257 warning("You must specify a mode through the --mode option.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	258 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	259 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	260 if (is.null(opt$mzprec)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	261 warning("You must set a precision in MZ with the --mzprec option.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	262 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	263 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	264 if ( ( ! is.null(opt$rtcol) \|\| ! is.null(opt[['all-cols']])) && (is.null(opt$rttolx) \|\| is.null(opt$rttoly))) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	265 warning("When chromatographic columns are set, you must provide values for --rttolx and -rttoly.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	266 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	267 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	268 if (is.null(opt$mztolunit) \|\| ( ! opt$mztolunit %in% MSDB.MZTOLUNIT.VALS)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	269 warning("You must specify an M/Z tolerance unit through the --mztolunit option.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	270 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	271 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	272 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	273
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	274 # help
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	275 if (error)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	276 print.help(spec, status = 1)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	277
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	278 return(opt)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	279 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	280
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	281 #####################################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	282 # CHECK DATABASE CONNECTION OPTIONS #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	283 #####################################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	284
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	285 .check.db.conn.opts <- function(opt) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	286
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	287 # Print default values
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	288 if ( ! is.null(opt[['print-db-fields']])) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	289 cat(MSDB.DFT[['db-fields']])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	290 q(status = 0)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	291 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	292 if ( ! is.null(opt[['print-db-ms-modes']])) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	293 cat(MSDB.DFT[['db-ms-modes']])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	294 q(status = 0)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	295 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	296
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	297 # Check values
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	298 error <- FALSE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	299 if (is.null(opt$database)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	300 warning("You must provide a database type through --database option.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	301 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	302 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	303 if ( ! opt$database %in% MSDB.VALS) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	304 warning(paste0("Invalid value \"", opt$database, "\" for --database option."))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	305 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	306 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	307 if (opt$database == MSDB.FILE) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	308 if (is.null(opt$url)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	309 warning("When using single file database, you must specify the location of the database file with option --url.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	310 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	311 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	312 if ( ! file.exists(opt$url)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	313 warning(paste0("The file path \"", opt$url,"\" specified with --db-file option is not valid."))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	314 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	315 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	316 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	317 if (opt$database == MSDB.XLS) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	318 if (is.null(opt$url)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	319 warning("When using Excel database, you must specify the location of the Excel files directory with option --url.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	320 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	321 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	322 if ( ! file.exists(opt$url)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	323 warning(paste0("The directory path \"", opt$url,"\" specified with --xls-dir option is not valid."))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	324 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	325 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	326 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	327 if (opt$database == MSDB.4TABSQL) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	328 if (is.null(opt$url)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	329 warning("When using 4Tab SQL database, you must specify the URL of the SQL server with option --url.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	330 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	331 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	332 if (is.null(opt[['db-name']])) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	333 warning("When using 4Tab SQL database, you must specify the database name through the --db-name option.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	334 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	335 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	336 if (is.null(opt[['db-user']])) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	337 warning("When using 4Tab SQL database, you must specify the database user through the --db-user option.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	338 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	339 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	340 if (is.null(opt[['db-password']])) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	341 warning("When using 4Tab SQL database, you must specify the database user password through the --db-password option.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	342 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	343 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	344 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	345 if (opt$database == MSDB.PEAKFOREST) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	346 if (is.null(opt$url)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	347 warning("When using PeakForest database, you must specify the URL of the PeakForest server with option --url.")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	348 error <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	349 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	350 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	351
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	352 return(error)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	353 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	354
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	355 #############################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	356 # DISPLAY COMMAND LINE HELP #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	357 #############################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	358
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	359 .disp.cmd.line.help <- function(optspec, opt, prog, error = FALSE) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	360
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	361 if ( ! is.null(opt$help) \|\| error ) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	362 cat(getopt(optspec, usage = TRUE, command = prog))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	363 q(status = 1)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	364 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	365 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	366
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	367 #################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	368 # LOAD DATABASE #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	369 #################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	370
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	371 .load.db <- function(opt) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	372
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	373 if (is.null(opt[['pos-prec']]) && is.null(opt[['neg-prec']])) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	374 precursors <- NULL
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	375 } else {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	376 precursors <- list()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	377 precursors[[MSDB.TAG.POS]] <- opt[['pos-prec']]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	378 precursors[[MSDB.TAG.NEG]] <- opt[['neg-prec']]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	379 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	380
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	381 db <- switch(opt$database,
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	382 peakforest = MsPeakForestDb$new(url = opt$url, useragent = USERAGENT, token = opt[['db-token']]),
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	383 xls = MsXlsDb$new(db_dir = opt$url, cache_dir = opt[['cache-dir']]),
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	384 '4tabsql' = Ms4TabSqlDb$new(host = extract.address(opt$url), port = extract.port(opt$url), dbname = opt[['db-name']], user = opt[['db-user']], password = opt[['db-password']]),
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	385 file = MsFileDb$new(file = opt$url),
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	386 NULL)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	387 db$setPrecursors(precursors)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	388 if (db$areDbFieldsSettable())
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	389 db$setDbFields(opt[['db-fields']])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	390 if (db$areDbMsModesSettable())
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	391 db$setDbMsModes(opt[['db-ms-modes']])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	392 db$addObservers(MsDbLogger$new())
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	393
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	394 return(db)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	395 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	396
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	397 ###############
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	398 # OUTPUT HTML #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	399 ###############
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	400
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	401 output.html <- function(db, main, peaks, file, opt, output.fields) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	402
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	403 # Replace public database IDs by URLs
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	404 if ( ! is.null(peaks) \|\| ! is.null(main)) {
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	405 # Conversion from extdb id field to extdb name
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	406 extdb2classdb = list()
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	407 extdb2classdb[MSDB.TAG.KEGG] = BIODB.KEGG
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	408 extdb2classdb[MSDB.TAG.HMDB] = BIODB.HMDB
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	409 extdb2classdb[MSDB.TAG.CHEBI] = BIODB.CHEBI
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	410 extdb2classdb[MSDB.TAG.PUBCHEM] = BIODB.PUBCHEMCOMP
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	411
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	412 # Loop on all dbs
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	413 for (extdb in c(MSDB.TAG.KEGG, MSDB.TAG.HMDB, MSDB.TAG.CHEBI, MSDB.TAG.PUBCHEM)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	414 field <- output.fields[[extdb]]
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	415 if ( ! is.null(peaks) && field %in% colnames(peaks))
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	416 peaks[[field]] <- vapply(peaks[[field]], function(id) if (is.na(id)) '' else paste0('<a href="', get.entry.url(class = extdb2classdb[[extdb]], accession = id, content.type = BIODB.HTML), '">', id, '</a>'), FUN.VALUE = '')
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	417 if ( ! is.null(main) && field %in% colnames(main))
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	418 main[[field]] <- vapply(main[[field]], function(ids) if (is.na(ids) \|\| nchar(ids) == 0) '' else paste(vapply(strsplit(ids, opt[['molids-sep']])[[1]], function(id) paste0('<a href="', get.entry.url(class = extdb2classdb[[extdb]], accession = id, content.type = BIODB.HTML), '">', id, '</a>'), FUN.VALUE = ''), collapse = opt[['molids-sep']]), FUN.VALUE = '')
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	419 }
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	420 }
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	421
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	422 # Write HTML
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	423 html <- HtmlWriter(file = file)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	424 html$writeBegTag('html')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	425 html$writeBegTag('header')
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	426 html$writeTag('meta', attr = c(charset = "UTF-8"))
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	427 html$writeTag('title', text = "LC/MS matching results")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	428 html$writeBegTag('style')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	429 html$write('table, th, td { border-collapse: collapse; }')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	430 html$write('table, th { border: 1px solid black; }')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	431 html$write('td { border-left: 1px solid black; border-right: 1px solid black; }')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	432 html$write('th, td { padding: 5px; }')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	433 html$write('th { background-color: LightBlue; }')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	434 html$write('tr:nth-child(even) { background-color: LemonChiffon; }')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	435 html$write('tr:nth-child(odd) { background-color: LightGreen; }')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	436 html$writeEndTag('style')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	437 html$writeEndTag('header')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	438 html$writeBegTag('body')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	439 html$writeTag('h1', text = "LC/MS matching")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	440
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	441 # Write parameters
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	442 html$writeTag('h2', text = "Parameters")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	443 html$writeBegTag('ul')
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	444 html$writeTag('li', text = paste0("Mode = ", opt$mode, "."))
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	445 html$writeTag('li', text = paste0("M/Z precision = ", opt$mzprec, "."))
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	446 html$writeTag('li', text = paste0("M/Z shift = ", opt$mzshift, "."))
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	447 html$writeTag('li', text = paste0("Precursor match = ", (if (is.null(opt[['precursor-match']])) "no" else "yes"), "."))
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	448 if ( ! is.null(opt[['precursor-match']])) {
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	449 html$writeTag('li', text = paste0("Positive precursors = ", paste0(opt[['pos-prec']], collapse = ', '), "."))
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	450 html$writeTag('li', text = paste0("Negative precursors = ", paste0(opt[['neg-prec']], collapse = ', '), "."))
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	451 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	452 if ( ! is.null(opt$rtcol)) {
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	453 html$writeTag('li', text = paste0("Columns = ", paste(opt$rtcol, collapse = ", "), "."))
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	454 html$writeTag('li', text = paste0("RTX = ", opt$rttolx, "."))
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	455 html$writeTag('li', text = paste0("RTY = ", opt$rttoly, "."))
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	456 if ( ! is.null(opt[['precursor-match']]))
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	457 html$writeTag('li', text = paste0("RTZ = ", opt[['precursor-rt-tol']], "."))
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	458 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	459 html$writeEndTag('ul')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	460
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	461 # Write results
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	462 html$writeTag('h2', text = "Results")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	463 results <- FALSE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	464 if ( ! is.null(main) && nrow(main) > 0 && is.null(opt[['no-main-table-in-html-output']])) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	465 html$writeTag('h3', text = "Main output")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	466 html$writeTable(main)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	467 results <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	468 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	469 if ( ! is.null(peaks) && nrow(peaks) > 0) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	470 html$writeTag('h3', text = "Matched peaks")
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	471 html$writeTable(peaks)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	472 results <- TRUE
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	473 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	474 if ( ! results)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	475 html$writeTag('p', 'None.')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	476
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	477 html$writeEndTag('body')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	478 html$writeEndTag('html')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	479 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	480
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	481 ########
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	482 # MAIN #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	483 ########
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	484
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	485 options(error = function() { traceback(2) ; quit(status = 1) }, warn = 2 )
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	486
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	487 # Read command line arguments
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	488 opt <- read_args()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	489
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	490 if (is.null(opt$debug)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	491 options(error = function() { quit(status = 1) }, warn = 0 )
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	492 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	493
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	494 # Load database
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	495 db <- .load.db(opt)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	496
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	497 # Print columns
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	498 if ( ! is.null(opt[['list-cols']])) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	499 cols <- db$getChromCol()
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	500 df.write.tsv(cols, file = if (is.null(opt[['output-file']])) stdout() else opt[['output-file']])
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	501 q(status = 0)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	502 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	503
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	504 # Read input
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	505 if ( ! is.null(opt[['input-file']]) && ! file.exists(opt[['input-file']]))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	506 stop(paste0("Input file \"", opt[['input-file']], "\" does not exist."))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	507 if (file.info(opt[['input-file']])$size > 0) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	508
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	509 # Load file into data frame
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	510 input <- read.table(file = opt[['input-file']], header = TRUE, sep = "\t", stringsAsFactor = FALSE)
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	511
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	512 # Convert each column that is identified by a number into a name
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	513 for (field in names(opt[['input-col-names']])) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	514 if ( ! opt[['input-col-names']][[field]] %in% colnames(input) && length(grep('^[0-9]+$', opt[['input-col-names']][[field]])) > 0) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	515 col.index <- as.integer(opt[['input-col-names']][[field]])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	516 if (col.index < 1 \|\| col.index > length(colnames(input)))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	517 stop(paste0("No column n°", col.index, " for input field ", field, "."))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	518 opt[['input-col-names']][[field]] <- colnames(input)[[col.index]]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	519 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	520 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	521 } else {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	522 input <- data.frame()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	523 input[[opt[['input-col-names']][['mz']]]] <- double()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	524 input[[opt[['input-col-names']][['rt']]]] <- double()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	525 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	526
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	527 # Check mz column
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	528 if ( ! opt[['input-col-names']][['mz']] %in% colnames(input))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	529 stop(paste0('No column named "', opt[['input-col-names']][['mz']], '" in input file.'))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	530
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	531 # Set columns 'all-cols' specified
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	532 if ( ! is.null(opt[['all-cols']]))
5 18254e8d1b72 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb-dirty prog parents: 4 diff changeset	533 opt$rtcol <- db$getChromCol()[['id']]
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	534
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	535 # Check chrom columns
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	536 if ( ! is.null(opt[['check-cols']]) && ! is.null(opt$rtcol)) {
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	537 dbcols <- db$getChromCol()[['id']]
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	538 unknown.cols <- opt$rtcol[ ! opt$rtcol %in% dbcols]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	539 if (length(unknown.cols) > 0) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	540 stop(paste0("Unknown chromatographic column", (if (length(unknown.cols) > 1) 's' else ''), ': ', paste(unknown.cols, collapse = ', '), ".\nAllowed chromatographic column names are:\n", paste(dbcols, collapse = "\n")))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	541 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	542 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	543
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	544 # Check that an RT column exists when using MZ/RT matching
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	545 if ( ! is.null(opt$rtcol) && ! opt[['input-col-names']][['rt']] %in% colnames(input))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	546 stop(paste0("You are running an MZ/RT match run on your input data, but no retention time column named '", opt[['input-col-names']][['rt']],"' can be found inside your input file."))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	547
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	548 # Set streams
4 1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	549 input.stream <- MsDbInputDataFrameStream$new(df = input, input.fields = opt[['input-col-names']], rtunit = opt[['rtunit']])
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	550 main.output <- MsDbOutputDataFrameStream$new(keep.unused = ! is.null(opt[['same-cols']]), output.fields = opt[['output-col-names']], one.line = ! is.null(opt[['same-rows']]), match.sep = opt[['molids-sep']], first.val = ! is.null(opt[['first-val']]), ascii = ! is.null(opt[['excel2011comp']]), nogreek = ! is.null(opt[['excel2011comp']]), noapostrophe = ! is.null(opt[['excel2011comp']]), noplusminus = ! is.null(opt[['excel2011comp']]))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	551 peaks.output <- MsDbOutputDataFrameStream$new(keep.unused = ! is.null(opt[['same-cols']]), output.fields = opt[['output-col-names']], first.val = ! is.null(opt[['first-val']]), ascii = ! is.null(opt[['excel2011comp']]), nogreek = ! is.null(opt[['excel2011comp']]), noapostrophe = ! is.null(opt[['excel2011comp']]), noplusminus = ! is.null(opt[['excel2011comp']]))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	552 invisible(db$setInputStream(input.stream))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	553 db$addOutputStreams(c(main.output, peaks.output))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	554
4 1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	555 # Set database units
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	556 db$setMzTolUnit(opt$mztolunit)
4 1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	557 if ( ! is.null(opt[['db-rt-unit']]) && opt$database == 'file')
1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 1 diff changeset	558 db$setRtUnit(opt[['db-rt-unit']])
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	559
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	560 # Search database
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	561 mode <- if (opt$mode == POS_MODE) MSDB.TAG.POS else MSDB.TAG.NEG
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	562 db$searchForMzRtList(mode = mode, shift = opt$mzshift, prec = opt$mzprec, rt.tol = opt$rttol, rt.tol.x = opt$rttolx, rt.tol.y = opt$rttoly, col = opt$rtcol, precursor.match = ! is.null(opt[['precursor-match']]), precursor.rt.tol = opt[['precursor-rt-tol']])
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	563
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	564 # Write output
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	565 main.output$moveColumnsToBeginning(colnames(input))
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	566 peaks.output$moveColumnsToBeginning(colnames(input))
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	567 # TODO Create a class MsDbOutputCsvFileStream
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	568 df.write.tsv(main.output$getDataFrame(), file = opt[['output-file']], row.names = FALSE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	569 if ( ! is.null(opt[['peak-output-file']]))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	570 # TODO Create a class MsDbOutputCsvFileStream
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	571 df.write.tsv(peaks.output$getDataFrame(), file = opt[['peak-output-file']], row.names = FALSE)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	572 if ( ! is.null(opt[['html-output-file']]))
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	573 # TODO Create a class MsDbOutputHtmlFileStream
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	574 output.html(db = db, main = main.output$getDataFrame(), peaks = peaks.output$getDataFrame(), file = opt[['html-output-file']], opt = opt, output.fields = opt[['output-col-names']])

Mercurial > repos > prog > lcmsmatching

annotate search-mz @ 5:18254e8d1b72 draft