ms2snoop: MS2snoop.R annotate

annotate MS2snoop.R @ 6:77abacd33c31 draft

planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80

author	workflow4metabolomics
date	Fri, 30 Sep 2022 16:18:56 +0000
parents	78d5a12406c2
children	2a1f120a6874

rev	line source
6 77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1 #' read and process mspurity W4M files
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	2 #' create a summary of fragment for each precursor and a graphics of peseudo
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	3 #' spectra + correlation on which checking of fragment is based on
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	4 #' V3 try to identify and process multiple files for 1 precursor which may
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	5 #' occur if different collision energy are used
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	6 #' V4 elimination of correlation = NA. Correlation is done with precursor, if
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	7 #' precursor is not present correlation with most intense peak
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	8 #' author: Jean-Francois Martin
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	9 #' V5 is versionned, lintR-compliant, packaged, unit-tested, documented and
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	10 #' tested against data from other labs.
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	11 #' new maintainer: Lain Pavot - lain.pavot@inrae.fr
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	12 #'
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	13 #' @import optparse
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	14 #'
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	15
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	16
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	17 get_version <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	18 cmd <- commandArgs(trailingOnly = FALSE)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	19 root <- dirname(gsub("--file=", "", cmd[grep("--file=", cmd)]))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	20 readme <- readLines(file.path(root, "README.md"))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	21 version_line <- readme[grepl(" * @version: ", readme, fixed = TRUE)]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	22 return(gsub(".*: ", "", version_line))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	23 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	24
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	25 defaults <- list(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	26 MS2SNOOP_VERSION = get_version(),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	27 MISSING_PARAMETER_ERROR = 1,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	28 BAD_PARAMETER_VALUE_ERROR = 2,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	29 MISSING_INPUT_FILE_ERROR = 3,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	30 NO_ANY_RESULT_ERROR = 255,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	31 DEFAULT_PRECURSOR_PATH = NULL,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	32 DEFAULT_FRAGMENTS_PATH = NULL,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	33 DEFAULT_COMPOUNDS_PATH = NULL,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	34 DEFAULT_OUTPUT_PATH = "compound_fragments_result.txt",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	35 DEFAULT_TOLMZ = 0.01,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	36 DEFAULT_TOLRT = 20,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	37 DEFAULT_MZDECIMAL = 3,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	38 DEFAULT_R_THRESHOLD = 0.85,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	39 DEFAULT_MINNUMBERSCAN = 8,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	40 DEFAULT_SEUIL_RA = 0.05,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	41 DEFAULT_FRAGMENTS_MATCH_DELTA = 10,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	42 DEFAULT_FRAGMENTS_MATCH_DELTA_UNIT = "ppm",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	43 DEFAULT_PDF_PATH = ""
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	44 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	45 env <- globalenv()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	46 for (default in names(defaults)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	47 assign(default, defaults[[default]], envir = env)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	48 lockBinding(default, env)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	49 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	50
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	51 ########################################################################
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	52
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	53 get_formulas <- function(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	54 mzref,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	55 spectra,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	56 processing_parameters,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	57 background = !TRUE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	58 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	59 if (is.vector(mzref) && length(mzref) > 1) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	60 return(lapply(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	61 mzref,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	62 function(mz) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	63 return(get_formulas(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	64 mzref = mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	65 spectra = spectra,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	66 processing_parameters = processing_parameters,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	67 background = background
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	68 ))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	69 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	70 ))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	71 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	72 input <- sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	73 "%s-%s.ms",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	74 gsub("[[:space:]]", "_", processing_parameters$c_name),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	75 mzref
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	76 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	77 create_ms_file(input, mzref, spectra, processing_parameters)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	78 output <- sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	79 "out/%s-%s.out",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	80 gsub("[[:space:]]", "_", processing_parameters$c_name),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	81 mzref
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	82 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	83 command <- sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	84 paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	85 "sirius",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	86 "--noCite",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	87 "--noSummaries",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	88 "--loglevel=WARNING",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	89 "-i='%s'",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	90 "-o='%s'",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	91 "tree",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	92 ## loglevel is not working taken into account during
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	93 ## sirius startup, so we filter outputs...
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	94 "2>&1 \| grep '^(WARNING\|SEVERE)'"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	95 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	96 input,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	97 output
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	98 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	99 verbose_catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	100 ">> Sirius is running %swith the command: %s\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	101 if (background) "in the background " else "",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	102 command
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	103 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	104 system(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	105 command,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	106 wait = !background,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	107 ignore.stdout = background,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	108 ignore.stderr = background
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	109 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	110 return(extract_sirius_results(output, spectra$mz, processing_parameters))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	111 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	112
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	113 create_ms_file <- function(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	114 path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	115 mzref,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	116 spectra,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	117 processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	118 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	119 file_content <- paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	120 sprintf(">compound %s", processing_parameters$c_name),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	121 sprintf(">ionization %s", processing_parameters$ionization),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	122 sprintf(">parentmass %s", mzref),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	123 sprintf(">formula %s", processing_parameters$elemcomposition),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	124 sep = "\n"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	125 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	126 displayed_file_content <- sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	127 "%s\n>collision\n%s",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	128 file_content,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	129 paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	130 sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	131 "%s %s",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	132 spectra[1:3, "mz"],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	133 spectra[1:3, "intensities"]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	134 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	135 collapse = "\n"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	136 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	137 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	138 if (nrow(spectra) > 3) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	139 displayed_file_content <- sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	140 "%s\n[... %s more rows of mz and intensities ...]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	141 displayed_file_content,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	142 nrow(spectra) - 3
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	143 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	144 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	145 catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	146 ">> MS file created for %s with content:\n%s\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	147 processing_parameters$c_name,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	148 displayed_file_content
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	149 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	150 file_content <- sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	151 "%s\n\n>collision\n%s",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	152 file_content,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	153 paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	154 paste(spectra$mz, spectra$intensities),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	155 collapse = "\n"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	156 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	157 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	158 cat(file_content, file = path, append = FALSE)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	159 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	160
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	161 extract_sirius_results <- function(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	162 output,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	163 mz_list,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	164 processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	165 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	166
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	167 delta <- processing_parameters$fragment_match_delta
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	168 delta_unit <- tolower(processing_parameters$fragment_match_delta_unit)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	169
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	170 output <- list.dirs(output, recursive = FALSE)[[1]]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	171
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	172 spectra_out_dir <- sprintf("%s/spectra", output)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	173 spectra_filename <- sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	174 "%s/%s",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	175 spectra_out_dir,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	176 list.files(spectra_out_dir)[[1]]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	177 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	178
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	179 trees_out_dir <- sprintf("%s/trees", output)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	180 trees_filename <- sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	181 "%s/%s",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	182 trees_out_dir,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	183 list.files(trees_out_dir)[[1]]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	184 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	185
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	186 if (!is.null(spectra_filename)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	187 sirius_results <- get_csv_or_tsv(spectra_filename)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	188 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	189 return(rep(NA, length(mz_list)))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	190 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	191 if (!is.null(trees_filename)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	192 sirius_results <- cbind(sirius_results, extract_sirius_ppm(trees_filename))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	193 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	194 return(rep(NA, length(mz_list)))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	195 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	196
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	197 fragment_matchings <- data.frame(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	198 formula = NA,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	199 ppm = NA,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	200 mz = mz_list,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	201 error = NA
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	202 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	203
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	204 sirius_results <- filter_sirius_with_delta(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	205 sirius_results = sirius_results,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	206 original_mz = fragment_matchings$mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	207 delta = delta,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	208 delta_unit = delta_unit
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	209 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	210
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	211 for (index in seq_len(nrow(sirius_results))) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	212 result <- sirius_results[index, ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	213 filter <- which(order(abs(fragment_matchings$mz - result$mz)) == 1)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	214 fragment_matchings[filter, "formula"] <- result$formula
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	215 fragment_matchings[filter, "ppm"] <- result$ppm
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	216 catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	217 "[OK] Fragment with m/z=%s matches %s with a difference of %s ppm\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	218 fragment_matchings[filter, "mz"], result$formula, result$ppm
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	219 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	220 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	221 return(fragment_matchings)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	222 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	223
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	224 filter_sirius_with_delta <- function(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	225 sirius_results,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	226 original_mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	227 delta,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	228 delta_unit
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	229 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	230 if (is.numeric(delta) && !is.na(delta) && delta > 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	231 if (delta_unit == "ppm") {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	232 filter <- abs(sirius_results$ppm) <= delta
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	233 fine <- which(filter)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	234 not_fine <- which(!filter)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	235 catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	236 paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	237 "[KO] fragment %s (m/z=%s) eleminated because ppm=%s is greater",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	238 "than delta=%s\n"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	239 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	240 sirius_results[not_fine, ]$formula,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	241 sirius_results[not_fine, ]$mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	242 sirius_results[not_fine, ]$ppm,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	243 delta
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	244 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	245 sirius_results <- sirius_results[fine, ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	246 } else if (delta_unit == "mz") {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	247 differences <- sapply(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	248 sirius_results$mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	249 function(mz) min(abs(original_mz - mz))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	250 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	251 fine <- which(sapply(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	252 sirius_results$mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	253 function(mz) any(abs(original_mz - mz) <= delta)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	254 ))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	255 not_fine <- which(sapply(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	256 sirius_results$mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	257 function(mz) all(abs(original_mz - mz) > delta)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	258 ))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	259 catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	260 paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	261 "[KO] fragment %s eleminated because mz difference=%s is",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	262 "greater than delta=%s\n"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	263 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	264 sirius_results[not_fine, ]$formula,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	265 differences[not_fine],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	266 delta
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	267 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	268 sirius_results <- sirius_results[fine, ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	269 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	270 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	271 return(sirius_results)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	272 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	273
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	274 extract_sirius_ppm <- function(path) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	275 json <- file(path, "r")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	276 suppressWarnings(json_lines <- readLines(json))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	277 close(json)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	278 json_lines <- json_lines[
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	279 grepl("\\s+\"(massDeviation\|recalibratedMass)\" :", json_lines)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	280 ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	281 json_lines <- gsub("^\\s+\"[^\"]+\" : \"?", "", json_lines)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	282 ppms <- json_lines[seq(1, length(json_lines), 2)]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	283 mz <- json_lines[seq(2, length(json_lines), 2)]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	284 ppms <- as.numeric(gsub(" ppm .*", "", ppms))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	285 mz <- as.numeric(gsub(",$", "", mz))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	286 ordered <- order(mz)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	287 return(list(ppm = ppms[ordered], recalibrated_mz = mz[ordered]))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	288 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	289
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	290 #' @title plot_pseudo_spectra
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	291 #' @param x
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	292 #' @param fid
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	293 #' @param sum_int
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	294 #' @param vmz
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	295 #' @param cor_abs_int
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	296 #' @param refcol
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	297 #' @param c_name
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	298 #' @description plot_pseudo_spectra
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	299 #' function to compute sum of intensities among scans for all
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	300 #' m/z kept (cor > r_threshold & minimum number of scans)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	301 #' and plot pseudo spectra
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	302 #' x dataframe scan X fragments with scans number in the 1st column and
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	303 #' ions in next with intensities
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	304 #' fid file id when several a precursor has been detected in several files
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	305 plot_pseudo_spectra <- function(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	306 x,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	307 fid,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	308 sum_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	309 vmz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	310 cor_abs_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	311 refcol,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	312 meaned_mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	313 processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	314 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	315 ## du fait de la difference de nombre de colonne entre la dataframe qui
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	316 ## inclue les scans en 1ere col, mzRef se decale de 1
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	317 refcol <- refcol - 1
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	318 ## compute relative intensities max=100%
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	319 rel_int <- sum_int[-1]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	320 rel_int <- rel_int / max(rel_int)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	321
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	322 if (processing_parameters$do_pdf) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	323 ## define max value on vertical axis (need to increase in order to plot the
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	324 ## label of fragments)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	325 ymax <- max(rel_int) + 0.2 * max(rel_int)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	326
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	327 par(mfrow = c(2, 1))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	328 plot(vmz, rel_int, type = "h", ylim = c(0, ymax),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	329 main = processing_parameters$c_name
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	330 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	331 ## low correl coef. will be display in grey
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	332 cor_low <- which(round(cor_abs_int, 2) < processing_parameters$r_threshold)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	333
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	334 lbmzcor <- sprintf("%s(r=%s)", vmz, round(cor_abs_int, 2))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	335
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	336 if (length(cor_low) > 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	337 text(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	338 vmz[cor_low],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	339 rel_int[cor_low],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	340 lbmzcor[cor_low],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	341 cex = 0.5,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	342 col = "grey",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	343 srt = 90,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	344 adj = 0
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	345 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	346 if (length(vmz) - length(cor_low) > 1) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	347 text(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	348 vmz[-c(refcol, cor_low)],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	349 rel_int[-c(refcol, cor_low)],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	350 lbmzcor[-c(refcol, cor_low)],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	351 cex = 0.6,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	352 col = 1,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	353 srt = 90,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	354 adj = 0
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	355 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	356 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	357 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	358 if (length(vmz) > 1) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	359 text(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	360 vmz[-c(refcol)],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	361 rel_int[-c(refcol)],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	362 lbmzcor[-c(refcol)],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	363 cex = 0.6,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	364 col = 1,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	365 srt = 90,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	366 adj = 0
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	367 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	368 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	369 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	370
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	371 text(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	372 vmz[refcol],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	373 rel_int[refcol],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	374 lbmzcor[refcol],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	375 cex = 0.8,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	376 col = 2,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	377 srt = 90,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	378 adj = 0
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	379 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	380 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	381
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	382 ## prepare result file
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	383 cor_valid <- (round(cor_abs_int, 2) >= processing_parameters$r_threshold)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	384
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	385 do_sirius <- TRUE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	386 verbose_catf("Checking sirius parameters...\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	387 if (is.null(processing_parameters$ionization)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	388 do_sirius <- FALSE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	389 verbose_catf("[KO] No ionization passed in parameter.\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	390 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	391 verbose_catf("[OK] Ionization=%s.\n", processing_parameters$ionization)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	392 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	393 if (is.na(processing_parameters$elemcomposition)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	394 do_sirius <- FALSE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	395 verbose_catf("[KO] Elemental composition is NA.\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	396 } else if (length(processing_parameters$elemcomposition) < 1) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	397 do_sirius <- FALSE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	398 verbose_catf("[KO] No elemental composition is provided.\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	399 } else if (processing_parameters$elemcomposition == "") {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	400 do_sirius <- FALSE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	401 verbose_catf("[KO] Elemental composition is an empty string.\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	402 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	403 verbose_catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	404 "[OK] Elemental composition=%s.\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	405 processing_parameters$elemcomposition
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	406 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	407 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	408
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	409 cp_res_length <- length(vmz)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	410 ppm <- rep(NA, cp_res_length)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	411 formulas <- rep(NA, cp_res_length)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	412 if (do_sirius) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	413 verbose_catf("Everything is ok, preparing for sirius.\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	414 formulas <- get_formulas(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	415 mzref = processing_parameters$mzref,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	416 spectra = data.frame(mz = meaned_mz, intensities = sum_int[-1]),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	417 processing_parameters = processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	418 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	419 if (nrow(formulas) == 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	420 catf("No formula found.\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	421 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	422 ppm <- formulas$ppm
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	423 formulas <- formulas$formula
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	424 catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	425 "Found %s formula for %s fragments\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	426 length(formulas[which(!(is.na(formulas)))]),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	427 cp_res_length
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	428 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	429 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	430 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	431 verbose_catf("Sirius cannot be run.\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	432 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	433 cp_res <- data.frame(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	434 rep(processing_parameters$c_name, cp_res_length),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	435 rep(processing_parameters$inchikey, cp_res_length),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	436 rep(processing_parameters$elemcomposition, cp_res_length),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	437 formulas,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	438 meaned_mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	439 ppm,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	440 rep(fid, cp_res_length),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	441 cor_abs_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	442 sum_int[-1],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	443 rel_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	444 cor_valid
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	445 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	446
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	447 colnames(cp_res) <- c(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	448 "compoundName",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	449 "inchikey",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	450 "elemcomposition",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	451 "fragment",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	452 "fragment_mz",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	453 "ppm",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	454 "fileid",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	455 "CorWithPrecursor",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	456 "AbsoluteIntensity",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	457 "relativeIntensity",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	458 "corValid"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	459 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	460 return(cp_res)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	461 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	462
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	463 #'
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	464 #' @title extract_fragments
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	465 #'
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	466 #' @param precursors the precursor list from mspurity
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	467 #' @param fragments the fragments list from ms purity
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	468 # ' @param mzref
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	469 # ' @param rtref
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	470 # ' @param c_name
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	471 # ' @param inchikey
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	472 # ' @param elemcomposition
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	473 #' @param processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	474 #' @returns
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	475 #'
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	476 #' @description
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	477 #' function for extraction of fragments corresponding to precursors
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	478 #' detected by MSPurity
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	479 extract_fragments <- function( ## nolint cyclocomp_linter
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	480 precursors,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	481 fragments,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	482 processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	483 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	484 ## filter precursor in the precursors file based on mz and rt in the
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	485 ## compound list
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	486 catf("processing %s\n", processing_parameters$c_name)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	487 verbose_catf("===\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	488 param <- processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	489 selected_precursors <- which(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	490 (abs(precursors$precurMtchMZ - param$mzref) <= param$tolmz)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	491 & (abs(precursors$precurMtchRT - param$rtref) <= param$tolrt)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	492 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	493 rm(param)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	494
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	495 verbose_catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	496 "> %s precursors selected with mz=%s±%s and rt=%s±%s\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	497 length(selected_precursors),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	498 processing_parameters$mzref,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	499 processing_parameters$tolmz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	500 processing_parameters$rtref,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	501 processing_parameters$tolrt
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	502 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	503
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	504 ## check if there is the precursor in the file
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	505
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	506 if (length(selected_precursors) < 1) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	507 cat("> non detected in precursor file\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	508 show_end_processing()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	509 return(NULL)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	510 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	511
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	512 precursors <- precursors[selected_precursors, ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	513
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	514 ## check if fragments corresponding to precursor are found in several
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	515 ## files (collision energy)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	516 ## this lead to a processing for each fileid
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	517 file_ids <- as.character(sort(unique(precursors$fileid)))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	518 if (length(file_ids) > 1) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	519 catf("> several files detected for this compounds :\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	520 } else if (length(file_ids) < 1 \|\| nrow(precursors) < 1) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	521 return(data.frame())
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	522 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	523
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	524 res_comp <- data.frame()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	525 for (curent_file_id in file_ids) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	526 curent_precursors <- precursors[precursors$fileid == curent_file_id, ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	527 selected_fragments <- fragments[
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	528 fragments$grpid %in% as.character(curent_precursors$grpid)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	529 & fragments$fileid == curent_file_id,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	530 ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	531 filtered_fragments <- selected_fragments[
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	532 selected_fragments$ra > processing_parameters$seuil_ra,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	533 ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	534 if (nrow(filtered_fragments) != 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	535 res_comp_by_file <- process_file(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	536 curent_file_id = curent_file_id,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	537 precursor_mz = curent_precursors$mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	538 filtered_fragments = filtered_fragments,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	539 processing_parameters = processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	540 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	541 if (!is.null(res_comp_by_file)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	542 res_comp <- rbind(res_comp, res_comp_by_file)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	543 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	544 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	545 catf("No fragment found for in fragment file\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	546 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	547 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	548 return(unique(res_comp))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	549 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	550
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	551 process_file <- function(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	552 curent_file_id,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	553 precursor_mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	554 filtered_fragments,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	555 processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	556 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	557 mznominal <- round(x = filtered_fragments$mz, digits = 0)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	558 meaned_mz <- round(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	559 aggregate(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	560 data.frame(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	561 mz = filtered_fragments$mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	562 mznominal = mznominal
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	563 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	564 list(mznominal),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	565 FUN = mean
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	566 )$mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	567 digits = processing_parameters$mzdecimal
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	568 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	569 filtered_fragments <- data.frame(filtered_fragments, mznominal)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	570
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	571 ## creation of cross table row=scan col=mz X=ra
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	572
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	573 vmz <- as.character(sort(unique(filtered_fragments$mznominal)))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	574
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	575 ds_abs_int <- create_ds_abs_int(vmz, filtered_fragments)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	576
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	577 if (global_debug) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	578 print(ds_abs_int)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	579 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	580
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	581 ## elimination of mz with less than min_number_scan scans (user defined
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	582 ## parameter)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	583 xmz <- rep(NA, ncol(ds_abs_int) - 1)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	584 sum_int <- rep(NA, ncol(ds_abs_int))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	585 nbxmz <- 0
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	586 nb_scan_check <- min(nrow(ds_abs_int), processing_parameters$min_number_scan)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	587
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	588 for (j in 2:ncol(ds_abs_int)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	589 sum_int[j] <- sum(ds_abs_int[j], na.rm = TRUE)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	590 if (sum(!is.na(ds_abs_int[[j]])) < nb_scan_check) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	591 nbxmz <- nbxmz + 1
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	592 xmz[nbxmz] <- j
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	593 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	594 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	595
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	596 xmz <- xmz[-which(is.na(xmz))]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	597 if (length(xmz) > 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	598 ds_abs_int <- ds_abs_int[, -c(xmz)]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	599 sum_int <- sum_int[-c(xmz)]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	600 ## liste des mz keeped decale de 1 avec ds_abs_int
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	601 vmz <- as.numeric(vmz[-c(xmz - 1)])
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	602 meaned_mz <- meaned_mz[-c(xmz - 1)]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	603 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	604
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	605 ## mz of precursor in data precursor to check correlation with
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	606 mz_prec <- paste0(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	607 "mz",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	608 round(mean(precursor_mz), processing_parameters$mzdecimal)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	609 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	610 ## reference ion for correlation computing = precursor OR maximum
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	611 ## intensity ion in precursor is not present
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	612 refcol <- which(colnames(ds_abs_int) == mz_prec)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	613 if (length(refcol) == 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	614 refcol <- which(sum_int == max(sum_int, na.rm = TRUE))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	615 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	616
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	617 if (processing_parameters$do_pdf) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	618 start_pdf(processing_parameters, curent_file_id)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	619 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	620
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	621 ## Pearson correlations between absolute intensities computing
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	622 cor_abs_int <- rep(NA, length(vmz))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	623
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	624 if (length(refcol) > 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	625 for (i in 2:length(ds_abs_int)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	626 cor_abs_int[i - 1] <- stats::cor(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	627 x = ds_abs_int[[refcol]],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	628 y = ds_abs_int[[i]],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	629 use = "pairwise.complete.obs",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	630 method = "pearson"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	631 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	632 debug_catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	633 "Correlation between %s and %s: %s\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	634 paste(ds_abs_int[[refcol]], collapse = ";"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	635 paste(ds_abs_int[[i]], collapse = ";"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	636 paste(cor_abs_int[i - 1], collapse = ";")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	637 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	638 if (processing_parameters$do_pdf) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	639 pdf_plot_ds_abs_int(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	640 processing_parameters$c_name,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	641 ds_abs_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	642 refcol,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	643 i,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	644 round(cor_abs_int[i - 1], 2)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	645 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	646 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	647 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	648 ## plot pseudo spectra
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	649 res_comp_by_file <- plot_pseudo_spectra(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	650 x = ds_abs_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	651 fid = curent_file_id,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	652 sum_int = sum_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	653 vmz = vmz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	654 cor_abs_int = cor_abs_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	655 refcol = refcol,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	656 meaned_mz = meaned_mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	657 processing_parameters = processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	658 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	659 catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	660 "%s has been processed and %s fragments have been found.\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	661 processing_parameters$c_name,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	662 nrow(res_comp_by_file)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	663 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	664 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	665 res_comp_by_file <- NULL
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	666 cat(">> non detected in fragments file \n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	667 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	668 show_end_processing()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	669 if (processing_parameters$do_pdf) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	670 end_pdf()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	671 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	672 return(res_comp_by_file)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	673 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	674
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	675 create_ds_abs_int <- function(vmz, filtered_fragments) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	676 verbose_catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	677 ">> fragments: %s\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	678 paste(vmz, collapse = " ")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	679 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	680 ds_abs_int <- create_int_mz(vmz[1], filtered_fragments)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	681 for (mz in vmz[-1]) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	682 int_mz <- create_int_mz(mz, filtered_fragments)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	683 ds_abs_int <- merge(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	684 x = ds_abs_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	685 y = int_mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	686 by.x = 1,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	687 by.y = 1,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	688 all.x = TRUE,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	689 all.y = TRUE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	690 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	691 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	692 return(ds_abs_int)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	693 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	694
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	695 create_int_mz <- function(mz, filtered_fragments) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	696 ## absolute intensity
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	697 int_mz <- filtered_fragments[
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	698 filtered_fragments$mznominal == mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	699 c("acquisitionNum", "i")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	700 ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	701 colnames(int_mz)[2] <- paste0("mz", mz)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	702 ## average intensities of mass in duplicate scans
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	703 comp_scans <- aggregate(x = int_mz, by = list(int_mz[[1]]), FUN = mean)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	704 return(comp_scans[, -1])
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	705 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	706
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	707 show_end_processing <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	708 verbose_catf("==========\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	709 cat("\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	710 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	711
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	712 start_pdf <- function(processing_parameters, curent_file_id) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	713 if (!dir.exists(processing_parameters$pdf_path)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	714 dir.create(processing_parameters$pdf_path, recursive = TRUE)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	715 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	716 pdf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	717 file = sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	718 "%s/%s_processing_file%s.pdf",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	719 processing_parameters$pdf_path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	720 processing_parameters$c_name,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	721 curent_file_id
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	722 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	723 width = 8,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	724 height = 11
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	725 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	726 par(mfrow = c(3, 2))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	727 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	728
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	729 pdf_plot_ds_abs_int <- function(c_name, ds_abs_int, refcol, i, r_coef) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	730 plot(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	731 ds_abs_int[[refcol]],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	732 ds_abs_int[[i]],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	733 xlab = colnames(ds_abs_int)[refcol],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	734 ylab = colnames(ds_abs_int)[i],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	735 main = sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	736 "%s corr coeff r=%s", c_name, r_coef
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	737 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	738 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	739 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	740 end_pdf <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	741 dev.off()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	742 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	743
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	744 set_global <- function(var, value) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	745 assign(var, value, envir = globalenv())
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	746 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	747
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	748 set_debug <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	749 set_global("global_debug", TRUE)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	750 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	751
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	752 unset_debug <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	753 set_global("global_debug", FALSE)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	754 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	755
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	756 set_verbose <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	757 set_global("global_verbose", TRUE)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	758 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	759
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	760 unset_verbose <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	761 set_global("global_verbose", FALSE)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	762 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	763
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	764 verbose_catf <- function(...) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	765 if (global_verbose) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	766 cat(sprintf(...), sep = "")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	767 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	768 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	769
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	770
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	771 debug_catf <- function(...) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	772 if (global_debug) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	773 cat(sprintf(...), sep = "")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	774 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	775 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	776
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	777 catf <- function(...) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	778 cat(sprintf(...), sep = "")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	779 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	780
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	781 create_parser <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	782 parser <- optparse::OptionParser()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	783 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	784 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	785 c("-v", "--verbose"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	786 action = "store_true",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	787 default = FALSE,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	788 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	789 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	790 "Print extra output"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	791 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	792 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	793 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	794 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	795 c("-V", "--version"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	796 action = "store_true",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	797 default = FALSE,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	798 help = "Prints version and exits"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	799 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	800 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	801 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	802 c("-d", "--debug"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	803 action = "store_true",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	804 default = FALSE,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	805 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	806 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	807 "Print debug outputs"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	808 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	809 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	810 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	811 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	812 c("-o", "--output"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	813 type = "character",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	814 default = DEFAULT_OUTPUT_PATH,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	815 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	816 help = "Path to the output file [default %default]"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	817 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	818 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	819 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	820 c("-p", "--precursors"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	821 type = "character",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	822 default = DEFAULT_PRECURSOR_PATH,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	823 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	824 help = "Path to the precursors file [default %default]"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	825 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	826 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	827 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	828 c("-f", "--fragments"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	829 type = "character",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	830 default = DEFAULT_FRAGMENTS_PATH,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	831 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	832 help = "Path to the fragments file [default %default]"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	833 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	834 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	835 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	836 c("-c", "--compounds"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	837 type = "character",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	838 default = DEFAULT_COMPOUNDS_PATH,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	839 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	840 help = "Path to the compounds file [default %default]"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	841 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	842 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	843 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	844 c("--tolmz"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	845 type = "numeric",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	846 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	847 default = DEFAULT_TOLMZ,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	848 metavar = "number",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	849 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	850 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	851 "Tolerance for MZ (in Dalton) to match the standard in the compounds"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	852 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	853 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	854 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	855 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	856 c("--tolrt"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	857 type = "integer",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	858 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	859 default = DEFAULT_TOLRT,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	860 metavar = "number",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	861 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	862 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	863 "RT (in seconds) to match the standard in the compounds"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	864 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	865 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	866 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	867 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	868 c("--seuil_ra"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	869 type = "numeric",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	870 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	871 default = DEFAULT_SEUIL_RA,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	872 metavar = "number",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	873 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	874 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	875 "relative intensity threshold"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	876 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	877 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	878 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	879 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	880 c("--mzdecimal"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	881 type = "integer",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	882 default = DEFAULT_MZDECIMAL,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	883 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	884 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	885 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	886 "Number of decimal to write for MZ"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	887 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	888 metavar = "number"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	889 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	890 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	891 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	892 c("--r_threshold"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	893 type = "integer",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	894 default = DEFAULT_R_THRESHOLD,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	895 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	896 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	897 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	898 "R-Pearson correlation threshold between precursor and fragment",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	899 "absolute intensity"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	900 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	901 metavar = "number"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	902 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	903 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	904 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	905 c("--min_number_scan"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	906 type = "numeric",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	907 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	908 default = DEFAULT_MINNUMBERSCAN,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	909 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	910 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	911 "Fragments are kept if there are found in a minimum number",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	912 "of min_number_scan scans"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	913 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	914 metavar = "number"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	915 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	916 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	917 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	918 c("--pdf_path"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	919 type = "character",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	920 default = DEFAULT_PDF_PATH,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	921 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	922 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	923 "PDF files output path"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	924 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	925 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	926 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	927 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	928 c("--ionization"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	929 type = "character",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	930 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	931 default = "None",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	932 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	933 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	934 "Which ionization to use for sirius"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	935 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	936 metavar = "character"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	937 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	938 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	939 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	940 c("--fragment_match_delta"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	941 type = "numeric",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	942 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	943 default = DEFAULT_FRAGMENTS_MATCH_DELTA,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	944 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	945 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	946 "Fragment match delta"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	947 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	948 metavar = "numeric"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	949 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	950 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	951 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	952 c("--fragment_match_delta_unit"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	953 type = "character",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	954 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	955 default = DEFAULT_FRAGMENTS_MATCH_DELTA_UNIT,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	956 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	957 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	958 "Fragment match delta"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	959 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	960 metavar = "character"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	961 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	962 return(parser)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	963 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	964
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	965 stop_with_status <- function(msg, status) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	966 sink(stderr())
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	967 message(sprintf("Error: %s", msg))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	968 message(sprintf("Error code: %s", status))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	969 sink(NULL)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	970 base::quit(status = status)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	971 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	972
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	973 check_args_validity <- function(args) { ## nolint cyclocomp_linter
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	974 if (length(args$output) == 0 \|\| nchar(args$output[1]) == 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	975 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	976 "Missing output parameters. Please set it with --output.",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	977 MISSING_PARAMETER_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	978 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	979 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	980 if (length(args$precursors) == 0 \|\| nchar(args$precursors[1]) == 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	981 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	982 "Missing precursors parameters. Please set it with --precursors.",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	983 MISSING_PARAMETER_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	984 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	985 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	986 if (length(args$fragments) == 0 \|\| nchar(args$fragments[1]) == 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	987 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	988 "Missing fragments parameters. Please set it with --fragments.",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	989 MISSING_PARAMETER_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	990 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	991 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	992 if (length(args$compounds) == 0 \|\| nchar(args$compounds[1]) == 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	993 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	994 "Missing compounds parameters. Please set it with --compounds.",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	995 MISSING_PARAMETER_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	996 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	997 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	998 if (!file.exists(args$precursors)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	999 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1000 sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1001 "Precursors file %s does not exist or cannot be accessed.",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1002 args$precursors
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1003 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1004 MISSING_INPUT_FILE_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1005 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1006 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1007 if (!file.exists(args$fragments)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1008 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1009 sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1010 "Fragments file %s does not exist or cannot be accessed.",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1011 args$fragments
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1012 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1013 MISSING_INPUT_FILE_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1014 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1015 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1016 if (!file.exists(args$compounds)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1017 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1018 sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1019 "Compounds file %s does not exist or cannot be accessed.",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1020 args$compounds
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1021 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1022 MISSING_INPUT_FILE_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1023 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1024 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1025 if (in_galaxy_env()) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1026 check_galaxy_args_validity(args)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1027 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1028 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1029
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1030 in_galaxy_env <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1031 sysvars <- Sys.getenv()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1032 sysvarnames <- names(sysvars)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1033 return(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1034 "_GALAXY_JOB_HOME_DIR" %in% sysvarnames
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1035 \|\| "_GALAXY_JOB_TMP_DIR" %in% sysvarnames
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1036 \|\| "GALAXY_MEMORY_MB" %in% sysvarnames
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1037 \|\| "GALAXY_MEMORY_MB_PER_SLOT" %in% sysvarnames
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1038 \|\| "GALAXY_SLOTS" %in% sysvarnames
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1039 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1040 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1041
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1042 check_galaxy_args_validity <- function(args) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1043 if (!file.exists(args$output)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1044 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1045 sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1046 "Output file %s does not exist or cannot be accessed.",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1047 args$output
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1048 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1049 MISSING_INPUT_FILE_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1050 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1051 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1052 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1053
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1054 get_csv_or_tsv <- function(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1055 path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1056 sep_stack = c("\t", ",", ";"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1057 sep_names = c("tab", "comma", "semicolon"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1058 header = TRUE,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1059 quote = "\""
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1060 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1061 sep <- determine_csv_or_tsv_sep(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1062 path = path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1063 sep_stack = sep_stack,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1064 header = header,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1065 quote = quote
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1066 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1067 verbose_catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1068 "%s separator has been determined for %s.\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1069 sep_names[sep_stack == sep],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1070 path
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1071 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1072 return(read.table(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1073 file = path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1074 sep = sep,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1075 header = header,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1076 quote = quote
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1077 ))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1078 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1079
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1080 determine_csv_or_tsv_sep <- function(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1081 path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1082 sep_stack = c("\t", ",", ";"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1083 header = TRUE,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1084 quote = "\""
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1085 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1086 count <- -1
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1087 best_sep <- sep_stack[1]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1088 for (sep in sep_stack) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1089 tryCatch({
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1090 table <- read.table(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1091 file = path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1092 sep = sep,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1093 header = header,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1094 quote = quote,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1095 nrows = 1
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1096 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1097 if (ncol(table) > count) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1098 count <- ncol(table)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1099 best_sep <- sep
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1100 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1101 })
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1102 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1103 return(best_sep)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1104 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1105
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1106 uniformize_columns <- function(df) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1107 cols <- colnames(df)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1108 for (func in c(tolower)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1109 cols <- func(cols)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1110 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1111 colnames(df) <- cols
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1112 return(df)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1113 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1114
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1115 handle_galaxy_param <- function(args) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1116 for (param in names(args)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1117 if (is.character(args[[param]])) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1118 args[[param]] <- gsub("__ob__", "[", args[[param]])
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1119 args[[param]] <- gsub("__cb__", "]", args[[param]])
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1120 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1121 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1122 return(args)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1123 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1124
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1125 zip_pdfs <- function(processing_parameters) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1126 if (processing_parameters$do_pdf) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1127 if (zip <- Sys.getenv("R_ZIPCMD", "zip") == "") {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1128 catf("R could not fin the zip executable. Trying luck: zip = \"zip\"")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1129 zip <- "zip"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1130 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1131 catf("Found zip executable at %s .", zip)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1132 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1133 utils::zip(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1134 processing_parameters$pdf_zip_path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1135 processing_parameters$pdf_path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1136 zip = zip
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1137 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1138 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1139 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1140
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1141 main <- function(args) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1142 if (args$version) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1143 catf("%s\n", MS2SNOOP_VERSION)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1144 base::quit(status = 0)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1145 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1146 if (in_galaxy_env()) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1147 print(sessionInfo())
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1148 cat("\n\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1149 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1150 check_args_validity(args)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1151 args <- handle_galaxy_param(args)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1152 if (args$ionization == "None") {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1153 args$ionization <- NULL
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1154 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1155 if (args$debug) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1156 set_debug()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1157 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1158 if (args$verbose) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1159 set_verbose()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1160 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1161 precursors <- get_csv_or_tsv(args$precursors)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1162 fragments <- get_csv_or_tsv(args$fragments)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1163 compounds <- get_csv_or_tsv(args$compounds)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1164
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1165 compounds <- uniformize_columns(compounds)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1166 mandatory_columns <- c(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1167 "compound_name",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1168 "mz",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1169 "rtsec",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1170 "inchikey"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1171 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1172 presents <- mandatory_columns %in% colnames(compounds)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1173 if (!all(presents)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1174 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1175 sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1176 "Some columns are missing: %s",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1177 paste(mandatory_columns[which(!presents)], collapse = ", ")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1178 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1179 BAD_PARAMETER_VALUE_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1180 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1181 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1182
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1183 res_all <- data.frame()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1184 processing_parameters <- list(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1185 min_number_scan = args$min_number_scan,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1186 mzdecimal = args$mzdecimal,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1187 r_threshold = args$r_threshold,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1188 seuil_ra = args$seuil_ra,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1189 tolmz = args$tolmz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1190 tolrt = args$tolrt,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1191 ionization = args$ionization,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1192 do_pdf = nchar(args$pdf_path) > 0,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1193 pdf_zip_path = args$pdf_path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1194 pdf_path = tempdir(),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1195 fragment_match_delta = args$fragment_match_delta,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1196 fragment_match_delta_unit = args$fragment_match_delta_unit
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1197 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1198 for (i in seq_len(nrow(compounds))) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1199 processing_parameters$mzref <- compounds[["mz"]][i]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1200 processing_parameters$rtref <- compounds[["rtsec"]][i]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1201 processing_parameters$c_name <- compounds[["compound_name"]][i]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1202 processing_parameters$inchikey <- compounds[["inchikey"]][i]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1203 processing_parameters$elemcomposition <- compounds[["elemcomposition"]][i]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1204 res_cor <- extract_fragments(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1205 precursors = precursors,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1206 fragments = fragments,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1207 processing_parameters = processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1208 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1209 if (!is.null(res_cor)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1210 res_all <- rbind(res_all, res_cor)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1211 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1212 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1213
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1214 if (nrow(res_all) == 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1215 stop_with_status("No result at all!", NO_ANY_RESULT_ERROR)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1216 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1217
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1218 write.table(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1219 x = res_all,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1220 file = args$output,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1221 sep = "\t",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1222 row.names = FALSE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1223 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1224 zip_pdfs(processing_parameters)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1225 unlink(processing_parameters$pdf_path, recursive = TRUE)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1226 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1227
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1228 global_debug <- FALSE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1229 global_verbose <- FALSE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1230 args <- optparse::parse_args(create_parser())
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1231 main(args)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1232
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1233 warnings()

Mercurial > repos > workflow4metabolomics > ms2snoop

annotate MS2snoop.R @ 6:77abacd33c31 draft