ms2snoop: MS2snoop.R annotate

annotate MS2snoop.R @ 7:2a1f120a6874 draft default tip

planemo upload commit d9b3849751af6f74e3371db0c3525dcd08728723

author	workflow4metabolomics
date	Tue, 10 Jan 2023 11:07:48 +0000
parents	77abacd33c31
children

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,
7 2a1f120a6874 planemo upload commit d9b3849751af6f74e3371db0c3525dcd08728723 workflow4metabolomics parents: 6 diff changeset	57 background = !TRUE,
2a1f120a6874 planemo upload commit d9b3849751af6f74e3371db0c3525dcd08728723 workflow4metabolomics parents: 6 diff changeset	58 show_sirius_outputs = !TRUE
6 77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	59 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	60 if (is.vector(mzref) && length(mzref) > 1) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	61 return(lapply(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	62 mzref,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	63 function(mz) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	64 return(get_formulas(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	65 mzref = mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	66 spectra = spectra,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	67 processing_parameters = processing_parameters,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	68 background = background
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 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	73 input <- sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	74 "%s-%s.ms",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	75 gsub("[[:space:]]", "_", processing_parameters$c_name),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	76 mzref
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	77 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	78 create_ms_file(input, mzref, spectra, processing_parameters)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	79 output <- sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	80 "out/%s-%s.out",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	81 gsub("[[:space:]]", "_", processing_parameters$c_name),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	82 mzref
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	83 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	84 command <- sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	85 paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	86 "sirius",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	87 "--noCite",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	88 "--noSummaries",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	89 "--loglevel=WARNING",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	90 "-i='%s'",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	91 "-o='%s'",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	92 "tree",
7 2a1f120a6874 planemo upload commit d9b3849751af6f74e3371db0c3525dcd08728723 workflow4metabolomics parents: 6 diff changeset	93 "2>&1"
6 77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	94 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	95 input,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	96 output
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	97 )
7 2a1f120a6874 planemo upload commit d9b3849751af6f74e3371db0c3525dcd08728723 workflow4metabolomics parents: 6 diff changeset	98 if (!show_sirius_outputs) {
2a1f120a6874 planemo upload commit d9b3849751af6f74e3371db0c3525dcd08728723 workflow4metabolomics parents: 6 diff changeset	99 ## loglevel is not taken into account during
2a1f120a6874 planemo upload commit d9b3849751af6f74e3371db0c3525dcd08728723 workflow4metabolomics parents: 6 diff changeset	100 ## sirius startup, so we filter outputs...
2a1f120a6874 planemo upload commit d9b3849751af6f74e3371db0c3525dcd08728723 workflow4metabolomics parents: 6 diff changeset	101 command <- paste(command, "\| grep '^(WARNING\|SEVERE)'")
2a1f120a6874 planemo upload commit d9b3849751af6f74e3371db0c3525dcd08728723 workflow4metabolomics parents: 6 diff changeset	102 }
6 77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	103 verbose_catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	104 ">> Sirius is running %swith the command: %s\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	105 if (background) "in the background " else "",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	106 command
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	107 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	108 system(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	109 command,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	110 wait = !background,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	111 ignore.stdout = background,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	112 ignore.stderr = background
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	113 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	114 return(extract_sirius_results(output, spectra$mz, processing_parameters))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	115 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	116
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	117 create_ms_file <- function(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	118 path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	119 mzref,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	120 spectra,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	121 processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	122 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	123 file_content <- paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	124 sprintf(">compound %s", processing_parameters$c_name),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	125 sprintf(">ionization %s", processing_parameters$ionization),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	126 sprintf(">parentmass %s", mzref),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	127 sprintf(">formula %s", processing_parameters$elemcomposition),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	128 sep = "\n"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	129 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	130 displayed_file_content <- sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	131 "%s\n>collision\n%s",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	132 file_content,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	133 paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	134 sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	135 "%s %s",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	136 spectra[1:3, "mz"],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	137 spectra[1:3, "intensities"]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	138 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	139 collapse = "\n"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	140 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	141 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	142 if (nrow(spectra) > 3) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	143 displayed_file_content <- sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	144 "%s\n[... %s more rows of mz and intensities ...]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	145 displayed_file_content,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	146 nrow(spectra) - 3
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	147 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	148 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	149 catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	150 ">> MS file created for %s with content:\n%s\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	151 processing_parameters$c_name,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	152 displayed_file_content
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	153 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	154 file_content <- sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	155 "%s\n\n>collision\n%s",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	156 file_content,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	157 paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	158 paste(spectra$mz, spectra$intensities),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	159 collapse = "\n"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	160 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	161 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	162 cat(file_content, file = path, append = FALSE)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	163 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	164
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	165 extract_sirius_results <- function(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	166 output,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	167 mz_list,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	168 processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	169 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	170
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	171 delta <- processing_parameters$fragment_match_delta
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	172 delta_unit <- tolower(processing_parameters$fragment_match_delta_unit)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	173
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	174 output <- list.dirs(output, recursive = FALSE)[[1]]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	175
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	176 spectra_out_dir <- sprintf("%s/spectra", output)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	177 spectra_filename <- sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	178 "%s/%s",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	179 spectra_out_dir,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	180 list.files(spectra_out_dir)[[1]]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	181 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	182
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	183 trees_out_dir <- sprintf("%s/trees", output)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	184 trees_filename <- sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	185 "%s/%s",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	186 trees_out_dir,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	187 list.files(trees_out_dir)[[1]]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	188 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	189
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	190 if (!is.null(spectra_filename)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	191 sirius_results <- get_csv_or_tsv(spectra_filename)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	192 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	193 return(rep(NA, length(mz_list)))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	194 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	195 if (!is.null(trees_filename)) {
7 2a1f120a6874 planemo upload commit d9b3849751af6f74e3371db0c3525dcd08728723 workflow4metabolomics parents: 6 diff changeset	196 extracted_ppm <- extract_sirius_ppm(trees_filename)
2a1f120a6874 planemo upload commit d9b3849751af6f74e3371db0c3525dcd08728723 workflow4metabolomics parents: 6 diff changeset	197 sirius_results <- cbind(sirius_results, extracted_ppm)
6 77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	198 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	199 return(rep(NA, length(mz_list)))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	200 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	201
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	202 fragment_matchings <- data.frame(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	203 formula = NA,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	204 ppm = NA,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	205 mz = mz_list,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	206 error = NA
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	207 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	208
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	209 sirius_results <- filter_sirius_with_delta(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	210 sirius_results = sirius_results,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	211 original_mz = fragment_matchings$mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	212 delta = delta,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	213 delta_unit = delta_unit
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	214 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	215
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	216 for (index in seq_len(nrow(sirius_results))) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	217 result <- sirius_results[index, ]
7 2a1f120a6874 planemo upload commit d9b3849751af6f74e3371db0c3525dcd08728723 workflow4metabolomics parents: 6 diff changeset	218 filter <- order(abs(fragment_matchings$mz - result$mz))[1]
6 77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	219 fragment_matchings[filter, "formula"] <- result$formula
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	220 fragment_matchings[filter, "ppm"] <- result$ppm
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	221 catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	222 "[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	223 fragment_matchings[filter, "mz"], result$formula, result$ppm
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	224 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	225 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	226 return(fragment_matchings)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	227 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	228
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	229 filter_sirius_with_delta <- function(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	230 sirius_results,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	231 original_mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	232 delta,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	233 delta_unit
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	234 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	235 if (is.numeric(delta) && !is.na(delta) && delta > 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	236 if (delta_unit == "ppm") {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	237 filter <- abs(sirius_results$ppm) <= delta
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	238 fine <- which(filter)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	239 not_fine <- which(!filter)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	240 catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	241 paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	242 "[KO] fragment %s (m/z=%s) eleminated because ppm=%s is greater",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	243 "than delta=%s\n"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	244 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	245 sirius_results[not_fine, ]$formula,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	246 sirius_results[not_fine, ]$mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	247 sirius_results[not_fine, ]$ppm,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	248 delta
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	249 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	250 sirius_results <- sirius_results[fine, ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	251 } else if (delta_unit == "mz") {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	252 differences <- sapply(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	253 sirius_results$mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	254 function(mz) min(abs(original_mz - mz))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	255 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	256 fine <- which(sapply(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	257 sirius_results$mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	258 function(mz) any(abs(original_mz - mz) <= delta)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	259 ))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	260 not_fine <- which(sapply(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	261 sirius_results$mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	262 function(mz) all(abs(original_mz - mz) > delta)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	263 ))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	264 catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	265 paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	266 "[KO] fragment %s eleminated because mz difference=%s is",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	267 "greater than delta=%s\n"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	268 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	269 sirius_results[not_fine, ]$formula,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	270 differences[not_fine],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	271 delta
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	272 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	273 sirius_results <- sirius_results[fine, ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	274 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	275 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	276 return(sirius_results)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	277 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	278
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	279 extract_sirius_ppm <- function(path) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	280 json <- file(path, "r")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	281 suppressWarnings(json_lines <- readLines(json))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	282 close(json)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	283 json_lines <- json_lines[
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	284 grepl("\\s+\"(massDeviation\|recalibratedMass)\" :", json_lines)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	285 ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	286 json_lines <- gsub("^\\s+\"[^\"]+\" : \"?", "", json_lines)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	287 ppms <- json_lines[seq(1, length(json_lines), 2)]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	288 mz <- json_lines[seq(2, length(json_lines), 2)]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	289 ppms <- as.numeric(gsub(" ppm .*", "", ppms))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	290 mz <- as.numeric(gsub(",$", "", mz))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	291 ordered <- order(mz)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	292 return(list(ppm = ppms[ordered], recalibrated_mz = mz[ordered]))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	293 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	294
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	295 #' @title plot_pseudo_spectra
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	296 #' @param x
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	297 #' @param fid
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	298 #' @param sum_int
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	299 #' @param vmz
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	300 #' @param cor_abs_int
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	301 #' @param refcol
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	302 #' @param c_name
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	303 #' @description plot_pseudo_spectra
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	304 #' function to compute sum of intensities among scans for all
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	305 #' m/z kept (cor > r_threshold & minimum number of scans)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	306 #' and plot pseudo spectra
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	307 #' x dataframe scan X fragments with scans number in the 1st column and
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	308 #' ions in next with intensities
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	309 #' fid file id when several a precursor has been detected in several files
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	310 plot_pseudo_spectra <- function(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	311 x,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	312 fid,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	313 sum_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	314 vmz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	315 cor_abs_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	316 refcol,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	317 meaned_mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	318 processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	319 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	320 ## du fait de la difference de nombre de colonne entre la dataframe qui
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	321 ## inclue les scans en 1ere col, mzRef se decale de 1
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	322 refcol <- refcol - 1
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	323 ## compute relative intensities max=100%
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	324 rel_int <- sum_int[-1]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	325 rel_int <- rel_int / 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 if (processing_parameters$do_pdf) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	328 ## define max value on vertical axis (need to increase in order to plot the
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	329 ## label of fragments)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	330 ymax <- max(rel_int) + 0.2 * max(rel_int)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	331
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	332 par(mfrow = c(2, 1))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	333 plot(vmz, rel_int, type = "h", ylim = c(0, ymax),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	334 main = processing_parameters$c_name
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	335 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	336 ## low correl coef. will be display in grey
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	337 cor_low <- which(round(cor_abs_int, 2) < processing_parameters$r_threshold)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	338
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	339 lbmzcor <- sprintf("%s(r=%s)", vmz, round(cor_abs_int, 2))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	340
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	341 if (length(cor_low) > 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	342 text(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	343 vmz[cor_low],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	344 rel_int[cor_low],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	345 lbmzcor[cor_low],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	346 cex = 0.5,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	347 col = "grey",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	348 srt = 90,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	349 adj = 0
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	350 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	351 if (length(vmz) - length(cor_low) > 1) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	352 text(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	353 vmz[-c(refcol, cor_low)],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	354 rel_int[-c(refcol, cor_low)],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	355 lbmzcor[-c(refcol, cor_low)],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	356 cex = 0.6,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	357 col = 1,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	358 srt = 90,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	359 adj = 0
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	360 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	361 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	362 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	363 if (length(vmz) > 1) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	364 text(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	365 vmz[-c(refcol)],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	366 rel_int[-c(refcol)],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	367 lbmzcor[-c(refcol)],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	368 cex = 0.6,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	369 col = 1,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	370 srt = 90,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	371 adj = 0
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	372 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	373 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	374 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	375
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	376 text(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	377 vmz[refcol],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	378 rel_int[refcol],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	379 lbmzcor[refcol],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	380 cex = 0.8,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	381 col = 2,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	382 srt = 90,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	383 adj = 0
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	384 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	385 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	386
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	387 ## prepare result file
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	388 cor_valid <- (round(cor_abs_int, 2) >= processing_parameters$r_threshold)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	389
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	390 do_sirius <- TRUE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	391 verbose_catf("Checking sirius parameters...\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	392 if (is.null(processing_parameters$ionization)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	393 do_sirius <- FALSE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	394 verbose_catf("[KO] No ionization passed in parameter.\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	395 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	396 verbose_catf("[OK] Ionization=%s.\n", processing_parameters$ionization)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	397 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	398 if (is.na(processing_parameters$elemcomposition)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	399 do_sirius <- FALSE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	400 verbose_catf("[KO] Elemental composition is NA.\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	401 } else if (length(processing_parameters$elemcomposition) < 1) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	402 do_sirius <- FALSE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	403 verbose_catf("[KO] No elemental composition is provided.\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	404 } else if (processing_parameters$elemcomposition == "") {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	405 do_sirius <- FALSE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	406 verbose_catf("[KO] Elemental composition is an empty string.\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	407 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	408 verbose_catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	409 "[OK] Elemental composition=%s.\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	410 processing_parameters$elemcomposition
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	411 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	412 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	413
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	414 cp_res_length <- length(vmz)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	415 ppm <- rep(NA, cp_res_length)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	416 formulas <- rep(NA, cp_res_length)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	417 if (do_sirius) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	418 verbose_catf("Everything is ok, preparing for sirius.\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	419 formulas <- get_formulas(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	420 mzref = processing_parameters$mzref,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	421 spectra = data.frame(mz = meaned_mz, intensities = sum_int[-1]),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	422 processing_parameters = processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	423 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	424 if (nrow(formulas) == 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	425 catf("No formula found.\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	426 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	427 ppm <- formulas$ppm
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	428 formulas <- formulas$formula
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	429 catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	430 "Found %s formula for %s fragments\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	431 length(formulas[which(!(is.na(formulas)))]),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	432 cp_res_length
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	433 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	434 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	435 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	436 verbose_catf("Sirius cannot be run.\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	437 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	438 cp_res <- data.frame(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	439 rep(processing_parameters$c_name, cp_res_length),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	440 rep(processing_parameters$inchikey, cp_res_length),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	441 rep(processing_parameters$elemcomposition, cp_res_length),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	442 formulas,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	443 meaned_mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	444 ppm,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	445 rep(fid, cp_res_length),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	446 cor_abs_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	447 sum_int[-1],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	448 rel_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	449 cor_valid
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	450 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	451
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	452 colnames(cp_res) <- c(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	453 "compoundName",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	454 "inchikey",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	455 "elemcomposition",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	456 "fragment",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	457 "fragment_mz",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	458 "ppm",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	459 "fileid",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	460 "CorWithPrecursor",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	461 "AbsoluteIntensity",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	462 "relativeIntensity",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	463 "corValid"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	464 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	465 return(cp_res)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	466 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	467
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	468 #'
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	469 #' @title extract_fragments
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	470 #'
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	471 #' @param precursors the precursor list from mspurity
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	472 #' @param fragments the fragments list from ms purity
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	473 # ' @param mzref
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	474 # ' @param rtref
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	475 # ' @param c_name
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	476 # ' @param inchikey
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	477 # ' @param elemcomposition
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	478 #' @param processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	479 #' @returns
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	480 #'
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	481 #' @description
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	482 #' function for extraction of fragments corresponding to precursors
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	483 #' detected by MSPurity
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	484 extract_fragments <- function( ## nolint cyclocomp_linter
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	485 precursors,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	486 fragments,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	487 processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	488 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	489 ## filter precursor in the precursors file based on mz and rt in the
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	490 ## compound list
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	491 catf("processing %s\n", processing_parameters$c_name)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	492 verbose_catf("===\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	493 param <- processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	494 selected_precursors <- which(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	495 (abs(precursors$precurMtchMZ - param$mzref) <= param$tolmz)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	496 & (abs(precursors$precurMtchRT - param$rtref) <= param$tolrt)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	497 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	498 rm(param)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	499
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	500 verbose_catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	501 "> %s precursors selected with mz=%s±%s and rt=%s±%s\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	502 length(selected_precursors),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	503 processing_parameters$mzref,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	504 processing_parameters$tolmz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	505 processing_parameters$rtref,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	506 processing_parameters$tolrt
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	507 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	508
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	509 ## check if there is the precursor in the file
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	510
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	511 if (length(selected_precursors) < 1) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	512 cat("> non detected in precursor file\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	513 show_end_processing()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	514 return(NULL)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	515 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	516
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	517 precursors <- precursors[selected_precursors, ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	518
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	519 ## check if fragments corresponding to precursor are found in several
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	520 ## files (collision energy)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	521 ## this lead to a processing for each fileid
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	522 file_ids <- as.character(sort(unique(precursors$fileid)))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	523 if (length(file_ids) > 1) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	524 catf("> several files detected for this compounds :\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	525 } else if (length(file_ids) < 1 \|\| nrow(precursors) < 1) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	526 return(data.frame())
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	527 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	528
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	529 res_comp <- data.frame()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	530 for (curent_file_id in file_ids) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	531 curent_precursors <- precursors[precursors$fileid == curent_file_id, ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	532 selected_fragments <- fragments[
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	533 fragments$grpid %in% as.character(curent_precursors$grpid)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	534 & fragments$fileid == curent_file_id,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	535 ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	536 filtered_fragments <- selected_fragments[
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	537 selected_fragments$ra > processing_parameters$seuil_ra,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	538 ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	539 if (nrow(filtered_fragments) != 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	540 res_comp_by_file <- process_file(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	541 curent_file_id = curent_file_id,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	542 precursor_mz = curent_precursors$mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	543 filtered_fragments = filtered_fragments,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	544 processing_parameters = processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	545 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	546 if (!is.null(res_comp_by_file)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	547 res_comp <- rbind(res_comp, res_comp_by_file)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	548 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	549 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	550 catf("No fragment found for in fragment file\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	551 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	552 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	553 return(unique(res_comp))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	554 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	555
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	556 process_file <- function(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	557 curent_file_id,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	558 precursor_mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	559 filtered_fragments,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	560 processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	561 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	562 mznominal <- round(x = filtered_fragments$mz, digits = 0)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	563 meaned_mz <- round(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	564 aggregate(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	565 data.frame(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	566 mz = filtered_fragments$mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	567 mznominal = mznominal
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	568 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	569 list(mznominal),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	570 FUN = mean
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	571 )$mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	572 digits = processing_parameters$mzdecimal
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	573 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	574 filtered_fragments <- data.frame(filtered_fragments, mznominal)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	575
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	576 ## creation of cross table row=scan col=mz X=ra
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	577
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	578 vmz <- as.character(sort(unique(filtered_fragments$mznominal)))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	579
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	580 ds_abs_int <- create_ds_abs_int(vmz, filtered_fragments)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	581
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	582 if (global_debug) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	583 print(ds_abs_int)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	584 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	585
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	586 ## elimination of mz with less than min_number_scan scans (user defined
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	587 ## parameter)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	588 xmz <- rep(NA, ncol(ds_abs_int) - 1)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	589 sum_int <- rep(NA, ncol(ds_abs_int))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	590 nbxmz <- 0
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	591 nb_scan_check <- min(nrow(ds_abs_int), processing_parameters$min_number_scan)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	592
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	593 for (j in 2:ncol(ds_abs_int)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	594 sum_int[j] <- sum(ds_abs_int[j], na.rm = TRUE)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	595 if (sum(!is.na(ds_abs_int[[j]])) < nb_scan_check) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	596 nbxmz <- nbxmz + 1
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	597 xmz[nbxmz] <- j
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	598 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	599 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	600
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	601 xmz <- xmz[-which(is.na(xmz))]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	602 if (length(xmz) > 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	603 ds_abs_int <- ds_abs_int[, -c(xmz)]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	604 sum_int <- sum_int[-c(xmz)]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	605 ## liste des mz keeped decale de 1 avec ds_abs_int
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	606 vmz <- as.numeric(vmz[-c(xmz - 1)])
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	607 meaned_mz <- meaned_mz[-c(xmz - 1)]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	608 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	609
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	610 ## mz of precursor in data precursor to check correlation with
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	611 mz_prec <- paste0(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	612 "mz",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	613 round(mean(precursor_mz), processing_parameters$mzdecimal)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	614 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	615 ## reference ion for correlation computing = precursor OR maximum
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	616 ## intensity ion in precursor is not present
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	617 refcol <- which(colnames(ds_abs_int) == mz_prec)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	618 if (length(refcol) == 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	619 refcol <- which(sum_int == max(sum_int, na.rm = TRUE))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	620 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	621
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	622 if (processing_parameters$do_pdf) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	623 start_pdf(processing_parameters, curent_file_id)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	624 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	625
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	626 ## Pearson correlations between absolute intensities computing
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	627 cor_abs_int <- rep(NA, length(vmz))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	628
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	629 if (length(refcol) > 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	630 for (i in 2:length(ds_abs_int)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	631 cor_abs_int[i - 1] <- stats::cor(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	632 x = ds_abs_int[[refcol]],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	633 y = ds_abs_int[[i]],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	634 use = "pairwise.complete.obs",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	635 method = "pearson"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	636 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	637 debug_catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	638 "Correlation between %s and %s: %s\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	639 paste(ds_abs_int[[refcol]], collapse = ";"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	640 paste(ds_abs_int[[i]], collapse = ";"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	641 paste(cor_abs_int[i - 1], collapse = ";")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	642 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	643 if (processing_parameters$do_pdf) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	644 pdf_plot_ds_abs_int(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	645 processing_parameters$c_name,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	646 ds_abs_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	647 refcol,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	648 i,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	649 round(cor_abs_int[i - 1], 2)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	650 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	651 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	652 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	653 ## plot pseudo spectra
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	654 res_comp_by_file <- plot_pseudo_spectra(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	655 x = ds_abs_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	656 fid = curent_file_id,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	657 sum_int = sum_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	658 vmz = vmz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	659 cor_abs_int = cor_abs_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	660 refcol = refcol,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	661 meaned_mz = meaned_mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	662 processing_parameters = processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	663 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	664 catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	665 "%s has been processed and %s fragments have been found.\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	666 processing_parameters$c_name,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	667 nrow(res_comp_by_file)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	668 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	669 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	670 res_comp_by_file <- NULL
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	671 cat(">> non detected in fragments file \n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	672 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	673 show_end_processing()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	674 if (processing_parameters$do_pdf) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	675 end_pdf()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	676 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	677 return(res_comp_by_file)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	678 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	679
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	680 create_ds_abs_int <- function(vmz, filtered_fragments) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	681 verbose_catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	682 ">> fragments: %s\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	683 paste(vmz, collapse = " ")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	684 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	685 ds_abs_int <- create_int_mz(vmz[1], filtered_fragments)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	686 for (mz in vmz[-1]) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	687 int_mz <- create_int_mz(mz, filtered_fragments)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	688 ds_abs_int <- merge(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	689 x = ds_abs_int,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	690 y = int_mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	691 by.x = 1,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	692 by.y = 1,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	693 all.x = TRUE,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	694 all.y = TRUE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	695 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	696 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	697 return(ds_abs_int)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	698 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	699
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	700 create_int_mz <- function(mz, filtered_fragments) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	701 ## absolute intensity
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	702 int_mz <- filtered_fragments[
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	703 filtered_fragments$mznominal == mz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	704 c("acquisitionNum", "i")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	705 ]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	706 colnames(int_mz)[2] <- paste0("mz", mz)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	707 ## average intensities of mass in duplicate scans
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	708 comp_scans <- aggregate(x = int_mz, by = list(int_mz[[1]]), FUN = mean)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	709 return(comp_scans[, -1])
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 show_end_processing <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	713 verbose_catf("==========\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	714 cat("\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	715 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	716
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	717 start_pdf <- function(processing_parameters, curent_file_id) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	718 if (!dir.exists(processing_parameters$pdf_path)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	719 dir.create(processing_parameters$pdf_path, recursive = TRUE)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	720 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	721 pdf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	722 file = sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	723 "%s/%s_processing_file%s.pdf",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	724 processing_parameters$pdf_path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	725 processing_parameters$c_name,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	726 curent_file_id
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	727 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	728 width = 8,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	729 height = 11
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	730 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	731 par(mfrow = c(3, 2))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	732 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	733
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	734 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	735 plot(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	736 ds_abs_int[[refcol]],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	737 ds_abs_int[[i]],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	738 xlab = colnames(ds_abs_int)[refcol],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	739 ylab = colnames(ds_abs_int)[i],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	740 main = sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	741 "%s corr coeff r=%s", c_name, r_coef
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 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	745 end_pdf <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	746 dev.off()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	747 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	748
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	749 set_global <- function(var, value) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	750 assign(var, value, envir = globalenv())
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	751 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	752
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	753 set_debug <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	754 set_global("global_debug", TRUE)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	755 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	756
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	757 unset_debug <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	758 set_global("global_debug", FALSE)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	759 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	760
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	761 set_verbose <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	762 set_global("global_verbose", TRUE)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	763 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	764
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	765 unset_verbose <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	766 set_global("global_verbose", FALSE)
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 verbose_catf <- function(...) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	770 if (global_verbose) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	771 cat(sprintf(...), sep = "")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	772 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	773 }
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 debug_catf <- function(...) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	777 if (global_debug) {
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
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	782 catf <- function(...) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	783 cat(sprintf(...), sep = "")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	784 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	785
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	786 create_parser <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	787 parser <- optparse::OptionParser()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	788 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	789 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	790 c("-v", "--verbose"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	791 action = "store_true",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	792 default = FALSE,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	793 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	794 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	795 "Print extra output"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	796 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	797 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	798 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	799 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	800 c("-V", "--version"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	801 action = "store_true",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	802 default = FALSE,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	803 help = "Prints version and exits"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	804 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	805 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	806 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	807 c("-d", "--debug"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	808 action = "store_true",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	809 default = FALSE,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	810 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	811 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	812 "Print debug outputs"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	813 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	814 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	815 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	816 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	817 c("-o", "--output"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	818 type = "character",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	819 default = DEFAULT_OUTPUT_PATH,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	820 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	821 help = "Path to the output file [default %default]"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	822 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	823 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	824 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	825 c("-p", "--precursors"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	826 type = "character",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	827 default = DEFAULT_PRECURSOR_PATH,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	828 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	829 help = "Path to the precursors file [default %default]"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	830 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	831 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	832 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	833 c("-f", "--fragments"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	834 type = "character",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	835 default = DEFAULT_FRAGMENTS_PATH,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	836 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	837 help = "Path to the fragments file [default %default]"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	838 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	839 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	840 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	841 c("-c", "--compounds"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	842 type = "character",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	843 default = DEFAULT_COMPOUNDS_PATH,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	844 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	845 help = "Path to the compounds file [default %default]"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	846 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	847 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	848 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	849 c("--tolmz"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	850 type = "numeric",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	851 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	852 default = DEFAULT_TOLMZ,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	853 metavar = "number",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	854 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	855 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	856 "Tolerance for MZ (in Dalton) to match the standard in the compounds"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	857 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	858 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	859 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	860 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	861 c("--tolrt"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	862 type = "integer",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	863 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	864 default = DEFAULT_TOLRT,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	865 metavar = "number",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	866 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	867 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	868 "RT (in seconds) to match the standard in the compounds"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	869 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	870 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	871 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	872 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	873 c("--seuil_ra"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	874 type = "numeric",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	875 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	876 default = DEFAULT_SEUIL_RA,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	877 metavar = "number",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	878 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	879 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	880 "relative intensity threshold"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	881 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	882 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	883 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	884 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	885 c("--mzdecimal"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	886 type = "integer",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	887 default = DEFAULT_MZDECIMAL,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	888 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	889 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	890 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	891 "Number of decimal to write for MZ"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	892 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	893 metavar = "number"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	894 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	895 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	896 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	897 c("--r_threshold"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	898 type = "integer",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	899 default = DEFAULT_R_THRESHOLD,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	900 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	901 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	902 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	903 "R-Pearson correlation threshold between precursor and fragment",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	904 "absolute intensity"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	905 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	906 metavar = "number"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	907 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	908 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	909 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	910 c("--min_number_scan"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	911 type = "numeric",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	912 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	913 default = DEFAULT_MINNUMBERSCAN,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	914 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	915 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	916 "Fragments are kept if there are found in a minimum number",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	917 "of min_number_scan scans"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	918 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	919 metavar = "number"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	920 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	921 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	922 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	923 c("--pdf_path"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	924 type = "character",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	925 default = DEFAULT_PDF_PATH,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	926 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	927 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	928 "PDF files output path"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	929 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	930 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	931 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	932 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	933 c("--ionization"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	934 type = "character",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	935 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	936 default = "None",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	937 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	938 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	939 "Which ionization to use for sirius"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	940 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	941 metavar = "character"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	942 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	943 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	944 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	945 c("--fragment_match_delta"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	946 type = "numeric",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	947 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	948 default = DEFAULT_FRAGMENTS_MATCH_DELTA,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	949 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	950 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	951 "Fragment match delta"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	952 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	953 metavar = "numeric"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	954 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	955 parser <- optparse::add_option(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	956 parser,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	957 c("--fragment_match_delta_unit"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	958 type = "character",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	959 action = "store",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	960 default = DEFAULT_FRAGMENTS_MATCH_DELTA_UNIT,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	961 help = paste(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	962 "[default %default]",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	963 "Fragment match delta"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	964 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	965 metavar = "character"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	966 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	967 return(parser)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	968 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	969
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	970 stop_with_status <- function(msg, status) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	971 sink(stderr())
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	972 message(sprintf("Error: %s", msg))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	973 message(sprintf("Error code: %s", status))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	974 sink(NULL)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	975 base::quit(status = status)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	976 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	977
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	978 check_args_validity <- function(args) { ## nolint cyclocomp_linter
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	979 if (length(args$output) == 0 \|\| nchar(args$output[1]) == 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	980 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	981 "Missing output parameters. Please set it with --output.",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	982 MISSING_PARAMETER_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	983 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	984 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	985 if (length(args$precursors) == 0 \|\| nchar(args$precursors[1]) == 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	986 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	987 "Missing precursors parameters. Please set it with --precursors.",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	988 MISSING_PARAMETER_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	989 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	990 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	991 if (length(args$fragments) == 0 \|\| nchar(args$fragments[1]) == 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	992 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	993 "Missing fragments parameters. Please set it with --fragments.",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	994 MISSING_PARAMETER_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	995 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	996 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	997 if (length(args$compounds) == 0 \|\| nchar(args$compounds[1]) == 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	998 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	999 "Missing compounds parameters. Please set it with --compounds.",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1000 MISSING_PARAMETER_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1001 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1002 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1003 if (!file.exists(args$precursors)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1004 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1005 sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1006 "Precursors file %s does not exist or cannot be accessed.",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1007 args$precursors
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1008 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1009 MISSING_INPUT_FILE_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1010 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1011 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1012 if (!file.exists(args$fragments)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1013 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1014 sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1015 "Fragments file %s does not exist or cannot be accessed.",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1016 args$fragments
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1017 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1018 MISSING_INPUT_FILE_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1019 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1020 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1021 if (!file.exists(args$compounds)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1022 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1023 sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1024 "Compounds file %s does not exist or cannot be accessed.",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1025 args$compounds
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1026 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1027 MISSING_INPUT_FILE_ERROR
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 if (in_galaxy_env()) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1031 check_galaxy_args_validity(args)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1032 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1033 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1034
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1035 in_galaxy_env <- function() {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1036 sysvars <- Sys.getenv()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1037 sysvarnames <- names(sysvars)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1038 return(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1039 "_GALAXY_JOB_HOME_DIR" %in% sysvarnames
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1040 \|\| "_GALAXY_JOB_TMP_DIR" %in% sysvarnames
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1041 \|\| "GALAXY_MEMORY_MB" %in% sysvarnames
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1042 \|\| "GALAXY_MEMORY_MB_PER_SLOT" %in% sysvarnames
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1043 \|\| "GALAXY_SLOTS" %in% sysvarnames
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1044 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1045 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1046
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1047 check_galaxy_args_validity <- function(args) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1048 if (!file.exists(args$output)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1049 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1050 sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1051 "Output file %s does not exist or cannot be accessed.",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1052 args$output
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1053 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1054 MISSING_INPUT_FILE_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1055 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1056 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1057 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1058
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1059 get_csv_or_tsv <- function(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1060 path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1061 sep_stack = c("\t", ",", ";"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1062 sep_names = c("tab", "comma", "semicolon"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1063 header = TRUE,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1064 quote = "\""
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1065 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1066 sep <- determine_csv_or_tsv_sep(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1067 path = path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1068 sep_stack = sep_stack,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1069 header = header,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1070 quote = quote
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1071 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1072 verbose_catf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1073 "%s separator has been determined for %s.\n",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1074 sep_names[sep_stack == sep],
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1075 path
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1076 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1077 return(read.table(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1078 file = path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1079 sep = sep,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1080 header = header,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1081 quote = quote
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1082 ))
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1083 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1084
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1085 determine_csv_or_tsv_sep <- function(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1086 path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1087 sep_stack = c("\t", ",", ";"),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1088 header = TRUE,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1089 quote = "\""
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1090 ) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1091 count <- -1
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1092 best_sep <- sep_stack[1]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1093 for (sep in sep_stack) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1094 tryCatch({
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1095 table <- read.table(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1096 file = path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1097 sep = sep,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1098 header = header,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1099 quote = quote,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1100 nrows = 1
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1101 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1102 if (ncol(table) > count) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1103 count <- ncol(table)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1104 best_sep <- sep
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1105 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1106 })
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1107 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1108 return(best_sep)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1109 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1110
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1111 uniformize_columns <- function(df) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1112 cols <- colnames(df)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1113 for (func in c(tolower)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1114 cols <- func(cols)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1115 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1116 colnames(df) <- cols
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1117 return(df)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1118 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1119
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1120 handle_galaxy_param <- function(args) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1121 for (param in names(args)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1122 if (is.character(args[[param]])) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1123 args[[param]] <- gsub("__ob__", "[", args[[param]])
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1124 args[[param]] <- gsub("__cb__", "]", args[[param]])
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1125 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1126 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1127 return(args)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1128 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1129
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1130 zip_pdfs <- function(processing_parameters) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1131 if (processing_parameters$do_pdf) {
7 2a1f120a6874 planemo upload commit d9b3849751af6f74e3371db0c3525dcd08728723 workflow4metabolomics parents: 6 diff changeset	1132 if ((zip <- Sys.getenv("R_ZIPCMD", "zip")) == "") {
6 77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1133 catf("R could not fin the zip executable. Trying luck: zip = \"zip\"")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1134 zip <- "zip"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1135 } else {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1136 catf("Found zip executable at %s .", zip)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1137 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1138 utils::zip(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1139 processing_parameters$pdf_zip_path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1140 processing_parameters$pdf_path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1141 zip = zip
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1142 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1143 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1144 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1145
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1146 main <- function(args) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1147 if (args$version) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1148 catf("%s\n", MS2SNOOP_VERSION)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1149 base::quit(status = 0)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1150 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1151 if (in_galaxy_env()) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1152 print(sessionInfo())
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1153 cat("\n\n")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1154 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1155 check_args_validity(args)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1156 args <- handle_galaxy_param(args)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1157 if (args$ionization == "None") {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1158 args$ionization <- NULL
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1159 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1160 if (args$debug) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1161 set_debug()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1162 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1163 if (args$verbose) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1164 set_verbose()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1165 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1166 precursors <- get_csv_or_tsv(args$precursors)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1167 fragments <- get_csv_or_tsv(args$fragments)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1168 compounds <- get_csv_or_tsv(args$compounds)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1169
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1170 compounds <- uniformize_columns(compounds)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1171 mandatory_columns <- c(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1172 "compound_name",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1173 "mz",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1174 "rtsec",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1175 "inchikey"
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1176 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1177 presents <- mandatory_columns %in% colnames(compounds)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1178 if (!all(presents)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1179 stop_with_status(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1180 sprintf(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1181 "Some columns are missing: %s",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1182 paste(mandatory_columns[which(!presents)], collapse = ", ")
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1183 ),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1184 BAD_PARAMETER_VALUE_ERROR
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1185 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1186 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1187
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1188 res_all <- data.frame()
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1189 processing_parameters <- list(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1190 min_number_scan = args$min_number_scan,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1191 mzdecimal = args$mzdecimal,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1192 r_threshold = args$r_threshold,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1193 seuil_ra = args$seuil_ra,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1194 tolmz = args$tolmz,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1195 tolrt = args$tolrt,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1196 ionization = args$ionization,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1197 do_pdf = nchar(args$pdf_path) > 0,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1198 pdf_zip_path = args$pdf_path,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1199 pdf_path = tempdir(),
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1200 fragment_match_delta = args$fragment_match_delta,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1201 fragment_match_delta_unit = args$fragment_match_delta_unit
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1202 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1203 for (i in seq_len(nrow(compounds))) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1204 processing_parameters$mzref <- compounds[["mz"]][i]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1205 processing_parameters$rtref <- compounds[["rtsec"]][i]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1206 processing_parameters$c_name <- compounds[["compound_name"]][i]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1207 processing_parameters$inchikey <- compounds[["inchikey"]][i]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1208 processing_parameters$elemcomposition <- compounds[["elemcomposition"]][i]
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1209 res_cor <- extract_fragments(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1210 precursors = precursors,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1211 fragments = fragments,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1212 processing_parameters = processing_parameters
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1213 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1214 if (!is.null(res_cor)) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1215 res_all <- rbind(res_all, res_cor)
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
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1219 if (nrow(res_all) == 0) {
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1220 stop_with_status("No result at all!", NO_ANY_RESULT_ERROR)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1221 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1222
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1223 write.table(
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1224 x = res_all,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1225 file = args$output,
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1226 sep = "\t",
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1227 row.names = FALSE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1228 )
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1229 zip_pdfs(processing_parameters)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1230 unlink(processing_parameters$pdf_path, recursive = TRUE)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1231 }
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1232
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1233 global_debug <- FALSE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1234 global_verbose <- FALSE
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1235 args <- optparse::parse_args(create_parser())
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1236 main(args)
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1237
77abacd33c31 planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80 workflow4metabolomics parents: 5 diff changeset	1238 warnings()

Mercurial > repos > workflow4metabolomics > ms2snoop

annotate MS2snoop.R @ 7:2a1f120a6874 draft default tip