ms2snoop: MS2snoop.R annotate

annotate MS2snoop.R @ 5:78d5a12406c2 draft

planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3

author	workflow4metabolomics
date	Fri, 05 Aug 2022 17:25:45 +0000
parents	856001213966
children	77abacd33c31

rev	line source
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	2 #' read and process mspurity W4M files
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	3 #' create a summary of fragment for each precursor and a graphics of peseudo
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	4 #' spectra + correlation on which checking of fragment is based on
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	5 #' V3 try to identify and process multiple files for 1 precursor which may
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	6 #' occur if different collision energy are used
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	7 #' V4 elimination of correlation = NA. Correlation is done with precursor, if
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	8 #' precursor is not present correlation with most intense peak
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	9 #' author: Jean-Francois Martin
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	10 #' V5 is versionned, lintR-compliant, packaged, unit-tested, documented and
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	11 #' tested against data from other labs.
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	12 #' new maintainer: Lain Pavot - lain.pavot@inrae.fr
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	13 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	14 #' @import optparse
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	15 #'
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	16
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	17
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	18 get_version <- function() {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	19 cmd <- commandArgs(trailingOnly = FALSE)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	20 root <- dirname(gsub("--file=", "", cmd[grep("--file=", cmd)]))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	21 readme <- readLines(file.path(root, "README.md"))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	22 version_line <- readme[grepl(" * @version: ", readme, fixed = TRUE)]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	23 return(gsub(".*: ", "", version_line))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	24 }
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	25
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	26 defaults <- list(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	27 MS2SNOOP_VERSION = get_version(),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	28 MISSING_PARAMETER_ERROR = 1,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	29 BAD_PARAMETER_VALUE_ERROR = 2,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	30 MISSING_INPUT_FILE_ERROR = 3,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	31 NO_ANY_RESULT_ERROR = 255,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	32 DEFAULT_PRECURSOR_PATH = NULL,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	33 DEFAULT_FRAGMENTS_PATH = NULL,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	34 DEFAULT_COMPOUNDS_PATH = NULL,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	35 DEFAULT_OUTPUT_PATH = "compound_fragments_result.txt",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	36 DEFAULT_TOLMZ = 0.01,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	37 DEFAULT_TOLRT = 20,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	38 DEFAULT_MZDECIMAL = 3,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	39 DEFAULT_R_THRESHOLD = 0.85,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	40 DEFAULT_MINNUMBERSCAN = 8,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	41 DEFAULT_SEUIL_RA = 0.05,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	42 DEFAULT_FRAGMENTS_MATCH_DELTA = 10,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	43 DEFAULT_FRAGMENTS_MATCH_DELTA_UNIT = "ppm",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	44 DEFAULT_PDF_PATH = ""
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	45 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	46 env <- globalenv()
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	47 for (default in names(defaults)) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	48 assign(default, defaults[[default]], envir = env)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	49 lockBinding(default, env)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	50 }
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	51
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	52 ########################################################################
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	53
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	54 get_formulas <- function(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	55 mzref,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	56 spectra,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	57 nominal_mz_list,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	58 processing_parameters,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	59 background = !TRUE
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	60 ) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	61 if (is.vector(mzref) && length(mzref) > 1) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	62 return(lapply(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	63 mzref,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	64 function(mz) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	65 return(get_formulas(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	66 mzref = mz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	67 spectra = spectra,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	68 nominal_mz_list = nominal_mz_list,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	69 processing_parameters = processing_parameters,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	70 background = background
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	71 ))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	72 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	73 ))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	74 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	75 input <- sprintf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	76 "%s-%s.ms",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	77 gsub("[[:space:]]", "_", processing_parameters$c_name),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	78 mzref
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	79 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	80 create_ms_file(input, mzref, spectra, processing_parameters)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	81 output <- sprintf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	82 "out/%s-%s.out",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	83 gsub("[[:space:]]", "_", processing_parameters$c_name),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	84 mzref
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	85 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	86 command <- sprintf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	87 paste(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	88 "sirius",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	89 "--noCite",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	90 "--noSummaries",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	91 "--loglevel=WARNING",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	92 "-i='%s'",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	93 "-o='%s'",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	94 "tree",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	95 ## loglevel is not working taken into account during
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	96 ## sirius startup, so we filter outputs...
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	97 "2>&1 \| grep '^(WARNING\|SEVERE)'"
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	98 ),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	99 input,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	100 output
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	101 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	102 verbose_catf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	103 ">> Sirius is running %swith the command: %s\n",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	104 if (background) "in the background " else "",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	105 command
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	106 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	107 system(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	108 command,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	109 wait = !background,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	110 ignore.stdout = background,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	111 ignore.stderr = background
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	112 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	113 return(extract_sirius_results(output, spectra$mz, processing_parameters))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	114 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	115
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	116 create_ms_file <- function(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	117 path,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	118 mzref,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	119 spectra,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	120 processing_parameters
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	121 ) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	122 file_content <- paste(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	123 sprintf(">compound %s", processing_parameters$c_name),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	124 sprintf(">ionization %s", processing_parameters$ionization),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	125 sprintf(">parentmass %s", mzref),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	126 sprintf(">formula %s", processing_parameters$elemcomposition),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	127 sep = "\n"
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	128 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	129 displayed_file_content <- sprintf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	130 "%s\n>collision\n%s",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	131 file_content,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	132 paste(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	133 sprintf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	134 "%s %s",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	135 spectra[1:3, "mz"],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	136 spectra[1:3, "intensities"]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	137 ),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	138 collapse = "\n"
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	139 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	140 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	141 if (nrow(spectra) > 3) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	142 displayed_file_content <- sprintf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	143 "%s\n[... %s more rows of mz and intensities ...]",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	144 displayed_file_content,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	145 nrow(spectra) - 3
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	146 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	147 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	148 catf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	149 ">> MS file created for %s with content:\n%s\n",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	150 processing_parameters$c_name,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	151 displayed_file_content
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	152 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	153 file_content <- sprintf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	154 "%s\n\n>collision\n%s",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	155 file_content,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	156 paste(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	157 sprintf("%s %s", spectra$mz, spectra$intensities),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	158 collapse = "\n"
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	159 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	160 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	161 cat(file_content, file = path, append = FALSE)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	162 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	163
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	164 extract_sirius_results <- function(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	165 output,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	166 mz_list,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	167 processing_parameters
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	168 ) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	169
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	170 delta <- processing_parameters$fragment_match_delta
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	171 delta_unit <- tolower(processing_parameters$fragment_match_delta_unit)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	172
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	173 output <- list.dirs(output, recursive = FALSE)[[1]]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	174
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	175 spectra_out_dir <- sprintf("%s/spectra", output)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	176 spectra_filename <- sprintf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	177 "%s/%s",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	178 spectra_out_dir,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	179 list.files(spectra_out_dir)[[1]]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	180 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	181
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	182 trees_out_dir <- sprintf("%s/trees", output)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	183 trees_filename <- sprintf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	184 "%s/%s",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	185 trees_out_dir,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	186 list.files(trees_out_dir)[[1]]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	187 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	188
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	189 if (!is.null(spectra_filename)) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	190 sirius_results <- get_csv_or_tsv(spectra_filename)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	191 } else {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	192 return(rep(NA, length(mz_list)))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	193 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	194 if (!is.null(trees_filename)) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	195 sirius_results <- cbind(sirius_results, extract_sirius_ppm(trees_filename))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	196 } else {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	197 return(rep(NA, length(mz_list)))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	198 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	199
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	200 fragment_matchings <- data.frame(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	201 formula = NA,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	202 ppm = NA,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	203 mz = mz_list,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	204 error = NA
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	205 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	206
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	207 sirius_results <- filter_sirius_with_delta(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	208 sirius_results = sirius_results,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	209 original_mz = fragment_matchings$mz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	210 delta = delta,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	211 delta_unit = delta_unit
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	212 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	213
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	214 for (index in seq_len(nrow(sirius_results))) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	215 result <- sirius_results[index, ]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	216 filter <- which(order(abs(fragment_matchings$mz - result$mz)) == 1)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	217 fragment_matchings[filter, "formula"] <- result$formula
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	218 fragment_matchings[filter, "ppm"] <- result$ppm
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	219 catf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	220 "[OK] Fragment with m/z=%s matches %s with a difference of %s ppm\n",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	221 fragment_matchings[filter, "mz"], result$formula, result$ppm
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	222 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	223 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	224 return(fragment_matchings)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	225 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	226
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	227 filter_sirius_with_delta <- function(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	228 sirius_results,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	229 original_mz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	230 delta,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	231 delta_unit
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	232 ) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	233 if (is.numeric(delta) && !is.na(delta) && delta > 0) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	234 if (delta_unit == "ppm") {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	235 filter <- abs(sirius_results$ppm) <= delta
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	236 fine <- which(filter)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	237 not_fine <- which(!filter)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	238 catf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	239 paste("[KO] fragment %s (m/z=%s) eleminated because ppm=%s is greater",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	240 "than delta=%s\n"
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	241 ),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	242 sirius_results[not_fine, ]$formula,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	243 sirius_results[not_fine, ]$mz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	244 sirius_results[not_fine, ]$ppm,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	245 delta
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	246 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	247 sirius_results <- sirius_results[fine, ]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	248 } else if (delta_unit == "mz") {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	249 differences <- sapply(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	250 sirius_results$mz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	251 function(mz) min(abs(original_mz - mz))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	252 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	253 fine <- which(sapply(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	254 sirius_results$mz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	255 function(mz) any(abs(original_mz - mz) <= delta)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	256 ))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	257 not_fine <- which(sapply(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	258 sirius_results$mz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	259 function(mz) all(abs(original_mz - mz) > delta)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	260 ))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	261 catf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	262 paste(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	263 "[KO] fragment %s eleminated because mz difference=%s is",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	264 "greater than delta=%s\n"
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	265 ),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	266 sirius_results[not_fine, ]$formula,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	267 differences[not_fine],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	268 delta
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	269 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	270 sirius_results <- sirius_results[fine, ]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	271 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	272 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	273 return(sirius_results)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	274 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	275
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	276 extract_sirius_ppm <- function(path) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	277 json <- file(path, "r")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	278 suppressWarnings(json_lines <- readLines(json))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	279 close(json)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	280 json_lines <- json_lines[
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	281 grepl("\\s+\"(massDeviation\|recalibratedMass)\" :", json_lines)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	282 ]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	283 json_lines <- gsub("^\\s+\"[^\"]+\" : \"?", "", json_lines)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	284 ppms <- json_lines[seq(1, length(json_lines), 2)]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	285 mz <- json_lines[seq(2, length(json_lines), 2)]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	286 ppms <- as.numeric(gsub(" ppm .*", "", ppms))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	287 mz <- as.numeric(gsub(",$", "", mz))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	288 ordered <- order(mz)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	289 return(list(ppm = ppms[ordered], recalibrated_mz = mz[ordered]))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	290 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	291
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	292 #' @title plot_pseudo_spectra
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	293 #' @param x
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	294 #' @param fid
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	295 #' @param sum_int
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	296 #' @param vmz
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	297 #' @param cor_abs_int
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	298 #' @param refcol
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	299 #' @param c_name
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	300 #' @description plot_pseudo_spectra
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	301 #' function to compute sum of intensities among scans for all
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	302 #' m/z kept (cor > r_threshold & minimum number of scans)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	303 #' and plot pseudo spectra
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	304 #' x dataframe scan X fragments with scans number in the 1st column and
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	305 #' ions in next with intensities
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	306 #' fid file id when several a precursor has been detected in several files
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	307 plot_pseudo_spectra <- function(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	308 x,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	309 fid,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	310 sum_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	311 vmz,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	312 cor_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	313 refcol,
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	314 meaned_mz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	315 processing_parameters
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	316 ) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	317 ## du fait de la difference de nombre de colonne entre la dataframe qui
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	318 ## inclue les scans en 1ere col, mzRef se decale de 1
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	319 refcol <- refcol - 1
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	320 ## compute relative intensities max=100%
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	321 rel_int <- sum_int[-1]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	322 rel_int <- rel_int / max(rel_int)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	323
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	324 if (processing_parameters$do_pdf) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	325 ## define max value on vertical axis (need to increase in order to plot the
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	326 ## label of fragments)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	327 ymax <- max(rel_int) + 0.2 * max(rel_int)
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	328
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	329 par(mfrow = c(2, 1))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	330 plot(vmz, rel_int, type = "h", ylim = c(0, ymax),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	331 main = processing_parameters$c_name
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	332 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	333 ## low correl coef. will be display in grey
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	334 cor_low <- which(round(cor_abs_int, 2) < processing_parameters$r_threshold)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	335
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	336 lbmzcor <- sprintf("%s(r=%s)", vmz, round(cor_abs_int, 2))
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	337
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	338 if (length(cor_low) > 0) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	339 text(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	340 vmz[cor_low],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	341 rel_int[cor_low],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	342 lbmzcor[cor_low],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	343 cex = 0.5,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	344 col = "grey",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	345 srt = 90,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	346 adj = 0
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	347 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	348 if (length(vmz) - length(cor_low) > 1) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	349 text(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	350 vmz[-c(refcol, cor_low)],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	351 rel_int[-c(refcol, cor_low)],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	352 lbmzcor[-c(refcol, cor_low)],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	353 cex = 0.6,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	354 col = 1,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	355 srt = 90,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	356 adj = 0
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	357 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	358 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	359 } else {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	360 if (length(vmz) > 1) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	361 text(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	362 vmz[-c(refcol)],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	363 rel_int[-c(refcol)],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	364 lbmzcor[-c(refcol)],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	365 cex = 0.6,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	366 col = 1,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	367 srt = 90,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	368 adj = 0
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	369 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	370 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	371 }
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	372
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	373 text(
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	374 vmz[refcol],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	375 rel_int[refcol],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	376 lbmzcor[refcol],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	377 cex = 0.8,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	378 col = 2,
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	379 srt = 90,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	380 adj = 0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	381 )
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	382 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	383
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	384 ## prepare result file
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	385 cor_valid <- (round(cor_abs_int, 2) >= processing_parameters$r_threshold)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	386
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	387 do_sirius <- TRUE
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	388 verbose_catf("Checking sirius parameters...\n")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	389 if (is.null(processing_parameters$ionization)) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	390 do_sirius <- FALSE
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	391 verbose_catf("[KO] No ionization passed in parameter.\n")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	392 } else {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	393 verbose_catf("[OK] Ionization=%s.\n", processing_parameters$ionization)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	394 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	395 if (is.na(processing_parameters$elemcomposition)) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	396 do_sirius <- FALSE
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	397 verbose_catf("[KO] Elemental composition is NA.\n")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	398 } else if (length(processing_parameters$elemcomposition) < 1) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	399 do_sirius <- FALSE
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	400 verbose_catf("[KO] No elemental composition is provided.\n")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	401 } else if (processing_parameters$elemcomposition == "") {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	402 do_sirius <- FALSE
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	403 verbose_catf("[KO] Elemental composition is an empty string.\n")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	404 } else {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	405 verbose_catf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	406 "[OK] Elemental composition=%s.\n",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	407 processing_parameters$elemcomposition
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	408 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	409 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	410
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	411 cp_res_length <- length(vmz)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	412 ppm <- rep(NA, cp_res_length)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	413 formulas <- rep(NA, cp_res_length)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	414 if (do_sirius) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	415 verbose_catf("Everything is ok, preparing for sirius.\n")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	416 formulas <- get_formulas(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	417 mzref = processing_parameters$mzref,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	418 spectra = data.frame(mz = meaned_mz, intensities = sum_int[-1]),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	419 nominal_mz_list = vmz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	420 processing_parameters = processing_parameters
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	421 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	422 if (nrow(formulas) == 0) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	423 catf("No formula found.\n")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	424 } else {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	425 ppm <- formulas$ppm
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	426 formulas <- formulas$formula
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	427 catf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	428 "Found %s formula for %s fragments\n",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	429 length(formulas[which(!(is.na(formulas)))]),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	430 cp_res_length
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	431 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	432 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	433 } else {
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	434 verbose_catf("Sirius cannot be run.\n")
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	435 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	436 cp_res <- data.frame(
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	437 rep(processing_parameters$c_name, cp_res_length),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	438 rep(processing_parameters$inchikey, cp_res_length),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	439 rep(processing_parameters$elemcomposition, cp_res_length),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	440 formulas,
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	441 vmz,
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	442 ppm,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	443 rep(fid, cp_res_length),
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	444 cor_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	445 sum_int[-1],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	446 rel_int,
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	447 cor_valid
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	448 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	449
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	450 colnames(cp_res) <- c(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	451 "compoundName",
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	452 "inchikey",
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	453 "elemcomposition",
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	454 "fragment",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	455 "fragment_mz",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	456 "ppm",
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	457 "fileid",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	458 "CorWithPrecursor",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	459 "AbsoluteIntensity",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	460 "relativeIntensity",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	461 "corValid"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	462 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	463 return(cp_res)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	464 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	465
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	466 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	467 #' @title extract_fragments
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	468 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	469 #' @param precursors the precursor list from mspurity
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	470 #' @param fragments the fragments list from ms purity
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	471 # ' @param mzref
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	472 # ' @param rtref
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	473 # ' @param c_name
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	474 # ' @param inchikey
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	475 # ' @param elemcomposition
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	476 #' @param processing_parameters
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	477 #' @returns
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	478 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	479 #' @description
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	480 #' function for extraction of fragments corresponding to precursors
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	481 #' detected by MSPurity
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	482 extract_fragments <- function( ## nolint cyclocomp_linter
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	483 precursors,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	484 fragments,
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	485 processing_parameters
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	486 ) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	487 ## filter precursor in the precursors file based on mz and rt in the
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	488 ## compound list
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	489 catf("processing %s\n", processing_parameters$c_name)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	490 verbose_catf("===\n")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	491 param <- processing_parameters
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	492 selected_precursors <- which(
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	493 (abs(precursors$precurMtchMZ - param$mzref) <= param$tolmz)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	494 & (abs(precursors$precurMtchRT - param$rtref) <= param$tolrt)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	495 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	496 rm(param)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	497
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	498 verbose_catf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	499 "> %s precursors selected with mz=%s±%s and rt=%s±%s\n",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	500 length(selected_precursors),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	501 processing_parameters$mzref,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	502 processing_parameters$tolmz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	503 processing_parameters$rtref,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	504 processing_parameters$tolrt
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	505 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	506
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	507 ## check if there is the precursor in the file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	508
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	509 if (length(selected_precursors) < 1) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	510 cat("> non detected in precursor file\n")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	511 show_end_processing()
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	512 return(NULL)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	513 }
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	514
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	515 precursors <- precursors[selected_precursors, ]
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	516
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	517 ## check if fragments corresponding to precursor are found in several
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	518 ## files (collision energy)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	519 ## this lead to a processing for each fileid
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	520 file_ids <- as.character(sort(unique(precursors$fileid)))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	521 if (length(file_ids) > 1) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	522 catf("> several files detected for this compounds :\n")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	523 } else if (length(file_ids) < 1 \|\| nrow(precursors) < 1) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	524 return(data.frame())
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	525 }
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	526
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	527 res_comp <- data.frame()
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	528 for (curent_file_id in file_ids) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	529 curent_precursors <- precursors[precursors$fileid == curent_file_id, ]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	530 selected_fragments <- fragments[
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	531 fragments$grpid %in% as.character(curent_precursors$grpid)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	532 & fragments$fileid == curent_file_id,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	533 ]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	534 filtered_fragments <- selected_fragments[
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	535 selected_fragments$ra > processing_parameters$seuil_ra,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	536 ]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	537 if (nrow(filtered_fragments) != 0) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	538 res_comp_by_file <- process_file(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	539 curent_file_id = curent_file_id,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	540 precursor_mz = curent_precursors$mz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	541 filtered_fragments = filtered_fragments,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	542 processing_parameters = processing_parameters
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	543 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	544 if (!is.null(res_comp_by_file)) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	545 res_comp <- rbind(res_comp, res_comp_by_file)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	546 }
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	547 } else {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	548 catf("No fragment found for in fragment file\n")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	549 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	550 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	551 return(unique(res_comp))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	552 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	553
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	554 process_file <- function(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	555 curent_file_id,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	556 precursor_mz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	557 filtered_fragments,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	558 processing_parameters
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	559 ) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	560 mznominal <- round(x = filtered_fragments$mz, digits = 0)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	561 meaned_mz <- round(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	562 aggregate(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	563 data.frame(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	564 mz = filtered_fragments$mz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	565 mznominal = mznominal
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	566 ),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	567 list(mznominal),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	568 FUN = mean
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	569 )$mz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	570 digits = processing_parameters$mzdecimal
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	571 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	572 filtered_fragments <- data.frame(filtered_fragments, mznominal)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	573
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	574 ## creation of cross table row=scan col=mz X=ra
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	575
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	576 vmz <- as.character(sort(unique(filtered_fragments$mznominal)))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	577
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	578 ds_abs_int <- create_ds_abs_int(vmz, filtered_fragments)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	579
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	580 if (global_debug) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	581 print(ds_abs_int)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	582 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	583
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	584 ## elimination of mz with less than min_number_scan scans (user defined
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	585 ## parameter)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	586 xmz <- rep(NA, ncol(ds_abs_int) - 1)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	587 sum_int <- rep(NA, ncol(ds_abs_int))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	588 nbxmz <- 0
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	589 nb_scan_check <- min(nrow(ds_abs_int), processing_parameters$min_number_scan)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	590
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	591 for (j in 2:ncol(ds_abs_int)) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	592 sum_int[j] <- sum(ds_abs_int[j], na.rm = TRUE)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	593 if (sum(!is.na(ds_abs_int[[j]])) < nb_scan_check) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	594 nbxmz <- nbxmz + 1
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	595 xmz[nbxmz] <- j
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	596 }
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	597 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	598
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	599 xmz <- xmz[-which(is.na(xmz))]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	600 if (length(xmz) > 0) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	601 ds_abs_int <- ds_abs_int[, -c(xmz)]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	602 sum_int <- sum_int[-c(xmz)]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	603 ## liste des mz keeped decale de 1 avec ds_abs_int
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	604 vmz <- as.numeric(vmz[-c(xmz - 1)])
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	605 meaned_mz <- meaned_mz[-c(xmz - 1)]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	606 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	607
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	608 ## mz of precursor in data precursor to check correlation with
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	609 mz_prec <- paste0(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	610 "mz",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	611 round(mean(precursor_mz), processing_parameters$mzdecimal)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	612 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	613 ## reference ion for correlation computing = precursor OR maximum
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	614 ## intensity ion in precursor is not present
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	615 refcol <- which(colnames(ds_abs_int) == mz_prec)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	616 if (length(refcol) == 0) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	617 refcol <- which(sum_int == max(sum_int, na.rm = TRUE))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	618 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	619
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	620 if (processing_parameters$do_pdf) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	621 start_pdf(processing_parameters, curent_file_id)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	622 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	623
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	624 ## Pearson correlations between absolute intensities computing
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	625 cor_abs_int <- rep(NA, length(vmz))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	626
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	627 if (length(refcol) > 0) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	628 for (i in 2:length(ds_abs_int)) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	629 cor_abs_int[i - 1] <- stats::cor(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	630 x = ds_abs_int[[refcol]],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	631 y = ds_abs_int[[i]],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	632 use = "pairwise.complete.obs",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	633 method = "pearson"
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	634 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	635 debug_catf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	636 "Correlation between %s and %s: %s\n",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	637 paste(ds_abs_int[[refcol]], collapse = ";"),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	638 paste(ds_abs_int[[i]], collapse = ";"),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	639 paste(cor_abs_int[i - 1], collapse = ";")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	640 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	641 if (processing_parameters$do_pdf) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	642 pdf_plot_ds_abs_int(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	643 processing_parameters$c_name,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	644 ds_abs_int,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	645 refcol,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	646 i,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	647 round(cor_abs_int[i - 1], 2)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	648 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	649 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	650 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	651 ## plot pseudo spectra
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	652 res_comp_by_file <- plot_pseudo_spectra(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	653 x = ds_abs_int,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	654 fid = curent_file_id,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	655 sum_int = sum_int,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	656 vmz = vmz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	657 cor_abs_int = cor_abs_int,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	658 refcol = refcol,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	659 meaned_mz = meaned_mz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	660 processing_parameters = processing_parameters
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	661 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	662 catf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	663 "%s has been processed and %s fragments have been found.\n",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	664 processing_parameters$c_name,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	665 nrow(res_comp_by_file)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	666 )
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	667 } else {
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	668 res_comp_by_file <- NULL
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	669 cat(">> non detected in fragments file \n")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	670 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	671 show_end_processing()
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	672 if (processing_parameters$do_pdf) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	673 end_pdf()
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	674 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	675 return(res_comp_by_file)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	676 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	677
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	678 create_ds_abs_int <- function(vmz, filtered_fragments) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	679 verbose_catf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	680 ">> fragments: %s\n",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	681 paste(vmz, collapse = " ")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	682 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	683 ds_abs_int <- create_int_mz(vmz[1], filtered_fragments)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	684 for (mz in vmz[-1]) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	685 int_mz <- create_int_mz(mz, filtered_fragments)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	686 ds_abs_int <- merge(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	687 x = ds_abs_int,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	688 y = int_mz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	689 by.x = 1,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	690 by.y = 1,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	691 all.x = TRUE,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	692 all.y = TRUE
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	693 )
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	694 }
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	695 return(ds_abs_int)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	696 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	697
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	698 create_int_mz <- function(mz, filtered_fragments) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	699 ## absolute intensity
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	700 int_mz <- filtered_fragments[
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	701 filtered_fragments$mznominal == mz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	702 c("acquisitionNum", "i")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	703 ]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	704 colnames(int_mz)[2] <- paste0("mz", mz)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	705 ## average intensities of mass in duplicate scans
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	706 comp_scans <- aggregate(x = int_mz, by = list(int_mz[[1]]), FUN = mean)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	707 return(comp_scans[, -1])
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	708 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	709
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	710 show_end_processing <- function() {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	711 verbose_catf("==========\n")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	712 cat("\n")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	713 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	714
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	715 start_pdf <- function(processing_parameters, curent_file_id) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	716 if (!dir.exists(processing_parameters$pdf_path)) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	717 dir.create(processing_parameters$pdf_path, recursive = TRUE)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	718 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	719 pdf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	720 file = sprintf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	721 "%s/%s_processing_file%s.pdf",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	722 processing_parameters$pdf_path,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	723 processing_parameters$c_name,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	724 curent_file_id
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	725 ),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	726 width = 8,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	727 height = 11
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	728 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	729 par(mfrow = c(3, 2))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	730 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	731
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	732 pdf_plot_ds_abs_int <- function(c_name, ds_abs_int, refcol, i, r_coef) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	733 plot(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	734 ds_abs_int[[refcol]],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	735 ds_abs_int[[i]],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	736 xlab = colnames(ds_abs_int)[refcol],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	737 ylab = colnames(ds_abs_int)[i],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	738 main = sprintf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	739 "%s corr coeff r=%s", c_name, r_coef
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	740 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	741 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	742 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	743 end_pdf <- function() {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	744 dev.off()
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	745 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	746
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	747 set_global <- function(var, value) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	748 assign(var, value, envir = globalenv())
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	749 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	750
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	751 set_debug <- function() {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	752 set_global("global_debug", TRUE)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	753 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	754
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	755 unset_debug <- function() {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	756 set_global("global_debug", FALSE)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	757 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	758
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	759 set_verbose <- function() {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	760 set_global("global_verbose", TRUE)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	761 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	762
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	763 unset_verbose <- function() {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	764 set_global("global_verbose", FALSE)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	765 }
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	766
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	767 verbose_catf <- function(...) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	768 if (global_verbose) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	769 cat(sprintf(...), sep = "")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	770 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	771 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	772
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	773
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	774 debug_catf <- function(...) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	775 if (global_debug) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	776 cat(sprintf(...), sep = "")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	777 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	778 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	779
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	780 catf <- function(...) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	781 cat(sprintf(...), sep = "")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	782 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	783
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	784 create_parser <- function() {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	785 parser <- optparse::OptionParser()
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	786 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	787 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	788 c("-v", "--verbose"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	789 action = "store_true",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	790 default = FALSE,
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	791 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	792 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	793 "Print extra output"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	794 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	795 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	796 parser <- optparse::add_option(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	797 parser,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	798 c("-V", "--version"),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	799 action = "store_true",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	800 default = FALSE,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	801 help = "Prints version and exits"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	802 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	803 parser <- optparse::add_option(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	804 parser,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	805 c("-d", "--debug"),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	806 action = "store_true",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	807 default = FALSE,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	808 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	809 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	810 "Print debug outputs"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	811 )
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	812 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	813 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	814 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	815 c("-o", "--output"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	816 type = "character",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	817 default = DEFAULT_OUTPUT_PATH,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	818 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	819 help = "Path to the output file [default %default]"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	820 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	821 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	822 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	823 c("-p", "--precursors"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	824 type = "character",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	825 default = DEFAULT_PRECURSOR_PATH,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	826 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	827 help = "Path to the precursors file [default %default]"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	828 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	829 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	830 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	831 c("-f", "--fragments"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	832 type = "character",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	833 default = DEFAULT_FRAGMENTS_PATH,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	834 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	835 help = "Path to the fragments file [default %default]"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	836 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	837 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	838 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	839 c("-c", "--compounds"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	840 type = "character",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	841 default = DEFAULT_COMPOUNDS_PATH,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	842 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	843 help = "Path to the compounds file [default %default]"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	844 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	845 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	846 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	847 c("--tolmz"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	848 type = "numeric",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	849 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	850 default = DEFAULT_TOLMZ,
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	851 metavar = "number",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	852 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	853 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	854 "Tolerance for MZ (in Dalton) to match the standard in the compounds"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	855 )
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	856 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	857 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	858 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	859 c("--tolrt"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	860 type = "integer",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	861 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	862 default = DEFAULT_TOLRT,
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	863 metavar = "number",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	864 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	865 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	866 "RT (in seconds) to match the standard in the compounds"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	867 )
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	868 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	869 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	870 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	871 c("--seuil_ra"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	872 type = "numeric",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	873 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	874 default = DEFAULT_SEUIL_RA,
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	875 metavar = "number",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	876 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	877 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	878 "relative intensity threshold"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	879 ),
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	880 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	881 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	882 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	883 c("--mzdecimal"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	884 type = "integer",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	885 default = DEFAULT_MZDECIMAL,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	886 action = "store",
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	887 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	888 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	889 "Number of decimal to write for MZ"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	890 ),
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	891 metavar = "number"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	892 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	893 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	894 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	895 c("--r_threshold"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	896 type = "integer",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	897 default = DEFAULT_R_THRESHOLD,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	898 action = "store",
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	899 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	900 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	901 "R-Pearson correlation threshold between precursor and fragment",
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	902 "absolute intensity"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	903 ),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	904 metavar = "number"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	905 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	906 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	907 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	908 c("--min_number_scan"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	909 type = "numeric",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	910 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	911 default = DEFAULT_MINNUMBERSCAN,
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	912 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	913 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	914 "Fragments are kept if there are found in a minimum number",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	915 "of min_number_scan scans"
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	916 ),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	917 metavar = "number"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	918 )
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	919 parser <- optparse::add_option(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	920 parser,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	921 c("--pdf_path"),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	922 type = "character",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	923 default = DEFAULT_PDF_PATH,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	924 help = paste(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	925 "[default %default]",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	926 "PDF files output path"
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	927 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	928 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	929 parser <- optparse::add_option(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	930 parser,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	931 c("--ionization"),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	932 type = "character",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	933 action = "store",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	934 default = "None",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	935 help = paste(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	936 "[default %default]",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	937 "Which ionization to use for sirius"
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	938 ),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	939 metavar = "character"
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	940 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	941 parser <- optparse::add_option(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	942 parser,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	943 c("--fragment_match_delta"),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	944 type = "numeric",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	945 action = "store",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	946 default = DEFAULT_FRAGMENTS_MATCH_DELTA,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	947 help = paste(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	948 "[default %default]",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	949 "Fragment match delta"
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	950 ),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	951 metavar = "numeric"
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	952 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	953 parser <- optparse::add_option(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	954 parser,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	955 c("--fragment_match_delta_unit"),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	956 type = "character",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	957 action = "store",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	958 default = DEFAULT_FRAGMENTS_MATCH_DELTA_UNIT,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	959 help = paste(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	960 "[default %default]",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	961 "Fragment match delta"
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	962 ),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	963 metavar = "character"
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	964 )
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	965 return(parser)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	966 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	967
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	968 stop_with_status <- function(msg, status) {
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	969 sink(stderr())
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	970 message(sprintf("Error: %s", msg))
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	971 message(sprintf("Error code: %s", status))
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	972 sink(NULL)
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	973 base::quit(status = status)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	974 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	975
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	976 check_args_validity <- function(args) { ## nolint cyclocomp_linter
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	977 if (length(args$output) == 0 \|\| nchar(args$output[1]) == 0) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	978 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	979 "Missing output parameters. Please set it with --output.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	980 MISSING_PARAMETER_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	981 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	982 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	983 if (length(args$precursors) == 0 \|\| nchar(args$precursors[1]) == 0) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	984 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	985 "Missing precursors parameters. Please set it with --precursors.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	986 MISSING_PARAMETER_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	987 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	988 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	989 if (length(args$fragments) == 0 \|\| nchar(args$fragments[1]) == 0) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	990 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	991 "Missing fragments parameters. Please set it with --fragments.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	992 MISSING_PARAMETER_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	993 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	994 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	995 if (length(args$compounds) == 0 \|\| nchar(args$compounds[1]) == 0) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	996 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	997 "Missing compounds parameters. Please set it with --compounds.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	998 MISSING_PARAMETER_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	999 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1000 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1001 if (!file.exists(args$precursors)) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1002 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1003 sprintf(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1004 "Precursors file %s does not exist or cannot be accessed.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1005 args$precursors
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1006 ),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1007 MISSING_INPUT_FILE_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1008 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1009 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1010 if (!file.exists(args$fragments)) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1011 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1012 sprintf(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1013 "Fragments file %s does not exist or cannot be accessed.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1014 args$fragments
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1015 ),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1016 MISSING_INPUT_FILE_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1017 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1018 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1019 if (!file.exists(args$compounds)) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1020 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1021 sprintf(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1022 "Compounds file %s does not exist or cannot be accessed.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1023 args$compounds
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1024 ),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1025 MISSING_INPUT_FILE_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1026 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1027 }
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1028 if (in_galaxy_env()) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1029 check_galaxy_args_validity(args)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1030 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1031 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1032
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1033 in_galaxy_env <- function() {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1034 sysvars <- Sys.getenv()
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1035 sysvarnames <- names(sysvars)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1036 return(
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1037 "_GALAXY_JOB_HOME_DIR" %in% sysvarnames
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1038 \|\| "_GALAXY_JOB_TMP_DIR" %in% sysvarnames
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1039 \|\| "GALAXY_MEMORY_MB" %in% sysvarnames
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1040 \|\| "GALAXY_MEMORY_MB_PER_SLOT" %in% sysvarnames
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1041 \|\| "GALAXY_SLOTS" %in% sysvarnames
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1042 )
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1043 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1044
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1045 check_galaxy_args_validity <- function(args) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1046 if (!file.exists(args$output)) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1047 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1048 sprintf(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1049 "Output file %s does not exist or cannot be accessed.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1050 args$output
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1051 ),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1052 MISSING_INPUT_FILE_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1053 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1054 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1055 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1056
3 c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	1057 get_csv_or_tsv <- function(
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	1058 path,
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	1059 sep_stack = c("\t", ",", ";"),
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1060 sep_names = c("tab", "comma", "semicolon"),
3 c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	1061 header = TRUE,
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	1062 quote = "\""
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	1063 ) {
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1064 sep <- determine_csv_or_tsv_sep(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1065 path = path,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1066 sep_stack = sep_stack,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1067 header = header,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1068 quote = quote
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1069 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1070 verbose_catf(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1071 "%s separator has been determined for %s.\n",
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1072 sep_names[sep_stack == sep],
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1073 path
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1074 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1075 return(read.table(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1076 file = path,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1077 sep = sep,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1078 header = header,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1079 quote = quote
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1080 ))
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1081 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1082
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1083 determine_csv_or_tsv_sep <- function(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1084 path,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1085 sep_stack = c("\t", ",", ";"),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1086 header = TRUE,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1087 quote = "\""
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1088 ) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1089 count <- -1
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1090 best_sep <- sep_stack[1]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1091 for (sep in sep_stack) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1092 tryCatch({
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1093 table <- read.table(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1094 file = path,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1095 sep = sep,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1096 header = header,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1097 quote = quote,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1098 nrows = 1
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1099 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1100 if (ncol(table) > count) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1101 count <- ncol(table)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1102 best_sep <- sep
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1103 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1104 })
3 c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	1105 }
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1106 return(best_sep)
3 c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	1107 }
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	1108
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1109 uniformize_columns <- function(df) {
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1110 cols <- colnames(df)
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1111 for (func in c(tolower)) {
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1112 cols <- func(cols)
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1113 }
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1114 colnames(df) <- cols
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1115 return(df)
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1116 }
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1117
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1118 handle_galaxy_param <- function(args) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1119 for (param in names(args)) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1120 if (is.character(args[[param]])) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1121 args[[param]] <- gsub("__ob__", "[", args[[param]])
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1122 args[[param]] <- gsub("__cb__", "]", args[[param]])
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1123 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1124 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1125 return(args)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1126 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1127
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1128 zip_pdfs <- function(processing_parameters) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1129 if (processing_parameters$do_pdf) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1130 if (zip <- Sys.getenv("R_ZIPCMD", "zip") == "") {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1131 catf("R could not fin the zip executable. Trying luck: zip = \"zip\"")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1132 zip <- "zip"
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1133 } else {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1134 catf("Found zip executable at %s .", zip)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1135 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1136 utils::zip(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1137 processing_parameters$pdf_zip_path,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1138 processing_parameters$pdf_path,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1139 zip = zip
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1140 )
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1141 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1142 }
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1143
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1144 main <- function(args) {
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1145 if (args$version) {
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1146 catf("%s\n", MS2SNOOP_VERSION)
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1147 base::quit(status = 0)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1148 }
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1149 if (in_galaxy_env()) {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1150 print(sessionInfo())
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1151 cat("\n\n")
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1152 }
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1153 check_args_validity(args)
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1154 args <- handle_galaxy_param(args)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1155 if (args$ionization == "None") {
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1156 args$ionization <- NULL
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1157 }
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1158 if (args$debug) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1159 set_debug()
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1160 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1161 if (args$verbose) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1162 set_verbose()
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1163 }
3 c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	1164 precursors <- get_csv_or_tsv(args$precursors)
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	1165 fragments <- get_csv_or_tsv(args$fragments)
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	1166 compounds <- get_csv_or_tsv(args$compounds)
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1167
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1168 compounds <- uniformize_columns(compounds)
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1169 mandatory_columns <- c(
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1170 "compound_name",
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1171 "mz",
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1172 "rtsec",
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1173 "inchikey"
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1174 )
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1175 presents <- mandatory_columns %in% colnames(compounds)
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1176 if (!all(presents)) {
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1177 stop_with_status(
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1178 sprintf(
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1179 "Some columns are missing: %s",
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1180 paste(mandatory_columns[which(!presents)], collapse = ", ")
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1181 ),
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1182 BAD_PARAMETER_VALUE_ERROR
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1183 )
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1184 }
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1185
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1186 res_all <- data.frame()
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1187 processing_parameters <- list(
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1188 min_number_scan = args$min_number_scan,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1189 mzdecimal = args$mzdecimal,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1190 r_threshold = args$r_threshold,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1191 seuil_ra = args$seuil_ra,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1192 tolmz = args$tolmz,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1193 tolrt = args$tolrt,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1194 ionization = args$ionization,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1195 do_pdf = nchar(args$pdf_path) > 0,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1196 pdf_zip_path = args$pdf_path,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1197 pdf_path = tempdir(),
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1198 fragment_match_delta = args$fragment_match_delta,
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1199 fragment_match_delta_unit = args$fragment_match_delta_unit
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1200 )
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1201 for (i in seq_len(nrow(compounds))) {
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1202 processing_parameters$mzref <- compounds[["mz"]][i]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1203 processing_parameters$rtref <- compounds[["rtsec"]][i]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1204 processing_parameters$c_name <- compounds[["compound_name"]][i]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1205 processing_parameters$inchikey <- compounds[["inchikey"]][i]
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1206 processing_parameters$elemcomposition <- compounds[["elemcomposition"]][i]
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1207 res_cor <- extract_fragments(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1208 precursors = precursors,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1209 fragments = fragments,
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1210 processing_parameters = processing_parameters
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1211 )
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1212 if (!is.null(res_cor)) {
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1213 res_all <- rbind(res_all, res_cor)
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1214 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1215 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1216
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1217 if (nrow(res_all) == 0) {
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	1218 stop_with_status("No result at all!", NO_ANY_RESULT_ERROR)
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1219 }
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1220
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1221 write.table(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1222 x = res_all,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1223 file = args$output,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1224 sep = "\t",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1225 row.names = FALSE
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1226 )
5 78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1227 zip_pdfs(processing_parameters)
78d5a12406c2 planemo upload commit a5f94dac9b268629399dc22c5d6ac48c5a85adc3 workflow4metabolomics parents: 4 diff changeset	1228 unlink(processing_parameters$pdf_path, recursive = TRUE)
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1229 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1230
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1231 global_debug <- FALSE
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	1232 global_verbose <- FALSE
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1233 args <- optparse::parse_args(create_parser())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1234 main(args)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1235
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	1236 warnings()

Mercurial > repos > workflow4metabolomics > ms2snoop

annotate MS2snoop.R @ 5:78d5a12406c2 draft