ms2snoop: MS2snoop.R annotate

annotate MS2snoop.R @ 2:a35fde23940e draft

planemo upload commit 7bb8dbe0a0bb34d897daf11c5dd3a92e89c23944

author	workflow4metabolomics
date	Wed, 08 Jun 2022 12:37:53 +0000
parents	df2672c37732
children	c68c94865667

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
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	18 assign("MS2SNOOP_VERSION", "1.0.1")
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	19 lockBinding("MS2SNOOP_VERSION", globalenv())
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	20
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	21 assign("MISSING_PARAMETER_ERROR", 1)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	22 lockBinding("MISSING_PARAMETER_ERROR", globalenv())
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	23
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	24 assign("BAD_PARAMETER_VALUE_ERROR", 2)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	25 lockBinding("BAD_PARAMETER_VALUE_ERROR", globalenv())
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	26
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	27 assign("MISSING_INPUT_FILE_ERROR", 3)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	28 lockBinding("MISSING_INPUT_FILE_ERROR", globalenv())
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	29
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	30 assign("NO_ANY_RESULT_ERROR", 255)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	31 lockBinding("NO_ANY_RESULT_ERROR", globalenv())
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	32
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	33 assign("DEFAULT_PRECURSOR_PATH", "peaklist_precursors.tsv")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	34 assign("DEFAULT_FRAGMENTS_PATH", "peaklist_fragments.tsv")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	35 assign("DEFAULT_COMPOUNDS_PATH", "compounds_pos.txt")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	36 assign("DEFAULT_OUTPUT_PATH", "compound_fragments_result.txt")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	37 assign("DEFAULT_TOLMZ", 0.01)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	38 assign("DEFAULT_TOLRT", 20)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	39 assign("DEFAULT_MZDECIMAL", 0)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	40 assign("DEFAULT_R_THRESHOLD", 0.85)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	41 assign("DEFAULT_MINNUMBERSCAN", 8)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	42 assign("DEFAULT_SEUIL_RA", 0.5)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	43 lockBinding("DEFAULT_PRECURSOR_PATH", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	44 lockBinding("DEFAULT_FRAGMENTS_PATH", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	45 lockBinding("DEFAULT_COMPOUNDS_PATH", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	46 lockBinding("DEFAULT_OUTPUT_PATH", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	47 lockBinding("DEFAULT_TOLMZ", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	48 lockBinding("DEFAULT_TOLRT", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	49 lockBinding("DEFAULT_MZDECIMAL", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	50 lockBinding("DEFAULT_R_THRESHOLD", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	51 lockBinding("DEFAULT_MINNUMBERSCAN", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	52 lockBinding("DEFAULT_SEUIL_RA", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	53
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	54 assign("DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD", 0.85)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	55 assign("DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA", 0.1)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	56 assign("DEFAULT_EXTRACT_FRAGMENTS_TOLMZ", 0.01)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	57 assign("DEFAULT_EXTRACT_FRAGMENTS_TOLRT", 60)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	58 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	59 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	60 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_TOLMZ", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	61 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_TOLRT", globalenv())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	62
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	63
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	64 ########################################################################
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	65
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	66 #' @title plot_pseudo_spectra
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	67 #' @param x
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	68 #' @param r_threshold
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	69 #' @param fid
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	70 #' @param sum_int
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	71 #' @param vmz
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	72 #' @param cor_abs_int
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	73 #' @param refcol
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	74 #' @param c_name
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	75 #' @description plot_pseudo_spectra
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	76 #' function to compute sum of intensities among scans for all
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	77 #' m/z kept (cor > r_threshold & minimum number of scans)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	78 #' and plot pseudo spectra
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	79 #' x dataframe scan X fragments with scans number in the 1st column and
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	80 #' ions in next with intensities
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	81 #' fid file id when several a precursor has been detected in several files
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	82 plot_pseudo_spectra <- function(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	83 x,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	84 r_threshold,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	85 fid,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	86 sum_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	87 vmz,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	88 cor_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	89 refcol,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	90 c_name
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	91 ) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	92 ## du fait de la difference de nombre de colonne entre la dataframe qui
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	93 ## inclue les scans en 1ere col, mzRef se decale de 1
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	94 refcol <- refcol - 1
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	95 ## compute relative intensities max=100%
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	96 rel_int <- sum_int[-1]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	97 rel_int <- rel_int / max(rel_int)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	98
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	99 ## define max value on vertical axis (need to increase in order to plot the
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	100 ## label of fragments)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	101 ymax <- max(rel_int) + 0.2 * max(rel_int)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	102
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	103 par(mfrow = c(2, 1))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	104 plot(vmz, rel_int, type = "h", ylim = c(0, ymax), main = c_name)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	105 ## low correl coef. will be display in grey
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	106 cor_low <- which(round(cor_abs_int, 2) < r_threshold)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	107
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	108 lbmzcor <- sprintf("%s(r=%s)", vmz, round(cor_abs_int, 2))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	109
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	110 if (length(cor_low) > 0) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	111 text(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	112 vmz[cor_low],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	113 rel_int[cor_low],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	114 lbmzcor[cor_low],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	115 cex = 0.5,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	116 col = "grey",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	117 srt = 90,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	118 adj = 0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	119 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	120 if (length(vmz) - length(cor_low) > 1) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	121 text(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	122 vmz[-c(refcol, cor_low)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	123 rel_int[-c(refcol, cor_low)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	124 lbmzcor[-c(refcol, cor_low)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	125 cex = 0.6,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	126 col = 1,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	127 srt = 90,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	128 adj = 0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	129 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	130 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	131 } else {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	132 if (length(vmz) > 1) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	133 text(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	134 vmz[-c(refcol)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	135 rel_int[-c(refcol)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	136 lbmzcor[-c(refcol)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	137 cex = 0.6,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	138 col = 1,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	139 srt = 90,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	140 adj = 0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	141 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	142 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	143 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	144
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	145 text(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	146 vmz[refcol],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	147 rel_int[refcol],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	148 lbmzcor[refcol],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	149 cex = 0.8,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	150 col = 2,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	151 srt = 90,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	152 adj = 0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	153 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	154
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	155 ## prepare result file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	156 corValid <- (round(cor_abs_int, 2) >= r_threshold) ##nolint object_name_linter
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	157 cp_res <- data.frame(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	158 rep(c_name, length(vmz)),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	159 rep(fid, length(vmz)),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	160 vmz,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	161 cor_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	162 sum_int[-1],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	163 rel_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	164 corValid
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	165 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	166
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	167 colnames(cp_res) <- c(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	168 "compoundName",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	169 "fileid",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	170 "fragments_mz",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	171 "CorWithPrecursor",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	172 "AbsoluteIntensity",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	173 "relativeIntensity",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	174 "corValid"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	175 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	176 return(cp_res)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	177
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	178 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	179
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	180 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	181 #' @title extract_fragments
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	182 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	183 #' @param precursors the precursor list from mspurity
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	184 #' @param fragments the fragments list from ms purity
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	185 #' @param mzref
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	186 #' @param rtref
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	187 #' @param c_name
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	188 #' @param r_threshold default = DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	189 #' @param seuil_ra default = DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	190 #' @param tolmz default = DEFAULT_EXTRACT_FRAGMENTS_TOLMZ
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	191 #' @param tolrt default = DEFAULT_EXTRACT_FRAGMENTS_TOLRT
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	192 #' @returns
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	193 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	194 #' @description
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	195 #' function for extraction of fragments corresponding to precursors
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	196 #' detected by MSPurity
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	197 extract_fragments <- function( ## nolint cyclocomp_linter
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	198 precursors,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	199 fragments,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	200 mzref,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	201 rtref,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	202 c_name,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	203 min_number_scan,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	204 mzdecimal,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	205 r_threshold=DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	206 seuil_ra=DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	207 tolmz=DEFAULT_EXTRACT_FRAGMENTS_TOLMZ,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	208 tolrt=DEFAULT_EXTRACT_FRAGMENTS_TOLRT
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	209 ) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	210 ## filter precursor in the precursors file based on mz and rt in the
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	211 ## compound list
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	212 cat("processing ", c_name, "\n")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	213 selected_precursors <- which(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	214 (abs(precursors$precurMtchMZ - mzref) <= tolmz)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	215 & (abs(precursors$precurMtchRT - rtref) <= tolrt)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	216 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	217
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	218 ## check if there is the precursor in the file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	219 if (length(selected_precursors) > 0) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	220
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	221 sprecini <- precursors[selected_precursors, ]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	222
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	223 ## check if fragments corresponding to precursor are found in several
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	224 ## files (collision energy)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	225 ## this lead to a processing for each fileid
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	226 mf <- levels(as.factor(sprecini$fileid))
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	227 if (length(mf) > 1 && global_verbose) {
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	228 cat(" several files detected for this compounds :\n")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	229 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	230
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	231 for (f in seq_along(mf)) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	232
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	233 sprec <- sprecini[sprecini$fileid == mf[f], ]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	234
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	235 ## selection of fragment in the fragments file with the grpid common in
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	236 ## both fragments and precursors
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	237 selfrgt <- levels(as.factor(sprec$grpid))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	238 sfrgt <- fragments[
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	239 fragments$grpid %in% selfrgt
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	240 & fragments$fileid == mf[f],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	241 ]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	242
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	243 ## filter fragments on relative intensity seuil_ra = user defined
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	244 ## parameter (MSpurity flags could be used here)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	245 sfrgtfil <- sfrgt[sfrgt$ra > seuil_ra, ]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	246
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	247 mznominal <- round(x = sfrgtfil$mz, mzdecimal)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	248 sfrgtfil <- data.frame(sfrgtfil, mznominal)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	249
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	250 ## creation of cross table row=scan col=mz X=ra
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	251 vmz <- levels(as.factor(sfrgtfil$mznominal))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	252
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	253 if (global_verbose) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	254 cat(" fragments :", vmz)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	255 }
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	256
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	257 ## mz of precursor in data precursor to check correlation with
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	258 mz_prec <- paste0("mz", round(mean(sprec$mz), mzdecimal))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	259
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	260 for (m in seq_along(vmz)) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	261
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	262 ## absolute intensity
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	263 cln <- c(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	264 which(colnames(sfrgtfil) == "acquisitionNum"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	265 which(colnames(sfrgtfil) == "i")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	266 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	267 int_mz <- sfrgtfil[sfrgtfil$mznominal == vmz[m], cln]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	268 colnames(int_mz)[2] <- paste0("mz", vmz[m])
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	269
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	270 ## average intensities of mass in duplicate scans
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	271 comp_scans <- aggregate(x = int_mz, by = list(int_mz[[1]]), FUN = mean)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	272 int_mz <- comp_scans[, -1]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	273
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	274 if (m == 1) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	275 ds_abs_int <- int_mz
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	276 } else {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	277 ds_abs_int <- merge(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	278 x = ds_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	279 y = int_mz,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	280 by.x = 1,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	281 by.y = 1,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	282 all.x = TRUE,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	283 all.y = TRUE
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	284 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	285 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	286 }
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	287 if (global_debug) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	288 print(ds_abs_int)
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	289 write.table(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	290 x = ds_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	291 file = paste0(c_name, "ds_abs_int.txt"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	292 row.names = FALSE,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	293 sep = "\t"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	294 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	295 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	296
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	297 ## elimination of mz with less than min_number_scan scans (user defined
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	298 ## parameter)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	299 xmz <- rep(NA, ncol(ds_abs_int) - 1)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	300 sum_int <- rep(NA, ncol(ds_abs_int))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	301 nbxmz <- 0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	302 nb_scan_check <- min(nrow(ds_abs_int), min_number_scan)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	303
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	304 for (j in 2:ncol(ds_abs_int)) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	305 sum_int[j] <- sum(ds_abs_int[j], na.rm = TRUE)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	306 if (sum(!is.na(ds_abs_int[[j]])) < nb_scan_check) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	307 nbxmz <- nbxmz + 1
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	308 xmz[nbxmz] <- j
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	309 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	310 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	311
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	312 xmz <- xmz[-which(is.na(xmz))]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	313 if (length(xmz) > 0) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	314 ds_abs_int <- ds_abs_int[, -c(xmz)]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	315 sum_int <- sum_int[-c(xmz)]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	316 ## liste des mz keeped decale de 1 avec ds_abs_int
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	317 vmz <- as.numeric(vmz[-c(xmz - 1)])
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	318 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	319
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	320 ## reference ion for correlation computing = precursor OR maximum
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	321 ## intensity ion in precursor is not present
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	322 refcol <- which(colnames(ds_abs_int) == mz_prec)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	323 if (length(refcol) == 0) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	324 refcol <- which(sum_int == max(sum_int, na.rm = TRUE))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	325 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	326 pdf(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	327 file = sprintf("%s_processing_file%s.pdf", c_name, mf[f]),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	328 width = 8,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	329 height = 11
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	330 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	331 par(mfrow = c(3, 2))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	332
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	333 ## Pearson correlations between absolute intensities computing
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	334 cor_abs_int <- rep(NA, length(vmz))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	335
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	336 if (length(refcol) > 0) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	337 for (i in 2:length(ds_abs_int)) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	338 cor_abs_int[i - 1] <- cor(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	339 x = ds_abs_int[[refcol]],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	340 y = ds_abs_int[[i]],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	341 use = "pairwise.complete.obs",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	342 method = "pearson"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	343 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	344 plot(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	345 ds_abs_int[[refcol]],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	346 ds_abs_int[[i]],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	347 xlab = colnames(ds_abs_int)[refcol],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	348 ylab = colnames(ds_abs_int)[i],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	349 main = sprintf(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	350 "%s corr coeff r=%s", c_name, round(cor_abs_int[i - 1], 2)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	351 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	352 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	353 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	354 ## plot pseudo spectra
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	355 res_comp_by_file <- plot_pseudo_spectra(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	356 x = ds_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	357 r_threshold = r_threshold,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	358 fid = mf[f],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	359 sum_int = sum_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	360 vmz = vmz,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	361 cor_abs_int = cor_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	362 refcol = refcol,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	363 c_name = c_name
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	364 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	365 if (f == 1) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	366 res_comp <- res_comp_by_file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	367 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	368 } else {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	369 res_comp_by_file <- NULL
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	370 cat(" non detected in fragments file \n")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	371 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	372 if (!is.null(res_comp_by_file)) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	373 res_comp <- rbind(res_comp, res_comp_by_file)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	374 }
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	375 if (global_verbose) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	376 cat("\n")
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	377 }
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	378 dev.off()
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	379 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	380 } else {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	381 res_comp <- NULL
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	382 cat(" non detected in precursor file \n")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	383 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	384 return(res_comp)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	385 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	386
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	387 set_global <- function(var, value) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	388 assign(var, value, envir = globalenv())
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	389 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	390
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	391 set_debug <- function() {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	392 set_global("global_debug", TRUE)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	393 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	394
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	395 unset_debug <- function() {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	396 set_global("global_debug", FALSE)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	397 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	398
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	399 set_verbose <- function() {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	400 set_global("global_verbose", TRUE)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	401 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	402
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	403 unset_verbose <- function() {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	404 set_global("global_verbose", FALSE)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	405 }
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	406
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	407 create_parser <- function() {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	408 parser <- optparse::OptionParser()
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	409 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	410 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	411 c("-v", "--verbose"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	412 action = "store_true",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	413 default = FALSE,
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	414 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	415 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	416 "Print extra output"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	417 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	418 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	419 parser <- optparse::add_option(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	420 parser,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	421 c("-V", "--version"),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	422 action = "store_true",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	423 default = FALSE,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	424 help = "Prints version and exits"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	425 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	426 parser <- optparse::add_option(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	427 parser,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	428 c("-d", "--debug"),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	429 action = "store_true",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	430 default = FALSE,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	431 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	432 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	433 "Print debug outputs"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	434 )
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	435 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	436 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	437 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	438 c("-o", "--output"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	439 type = "character",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	440 default = DEFAULT_OUTPUT_PATH,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	441 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	442 help = "Path to the output file [default %default]"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	443 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	444 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	445 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	446 c("-p", "--precursors"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	447 type = "character",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	448 default = DEFAULT_PRECURSOR_PATH,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	449 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	450 help = "Path to the precursors file [default %default]"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	451 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	452 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	453 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	454 c("-f", "--fragments"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	455 type = "character",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	456 default = DEFAULT_FRAGMENTS_PATH,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	457 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	458 help = "Path to the fragments file [default %default]"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	459 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	460 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	461 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	462 c("-c", "--compounds"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	463 type = "character",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	464 default = DEFAULT_COMPOUNDS_PATH,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	465 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	466 help = "Path to the compounds file [default %default]"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	467 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	468 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	469 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	470 c("--tolmz"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	471 type = "numeric",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	472 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	473 default = DEFAULT_TOLMZ,
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	474 metavar = "number",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	475 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	476 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	477 "Tolerance for MZ (in Dalton) to match the standard in the compounds"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	478 )
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	479 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	480 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	481 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	482 c("--tolrt"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	483 type = "integer",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	484 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	485 default = DEFAULT_TOLRT,
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	486 metavar = "number",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	487 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	488 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	489 "RT (in seconds) to match the standard in the compounds"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	490 )
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	491 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	492 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	493 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	494 c("--seuil_ra"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	495 type = "numeric",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	496 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	497 default = DEFAULT_SEUIL_RA,
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	498 metavar = "number",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	499 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	500 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	501 "relative intensity threshold"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	502 ),
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	503 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	504 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	505 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	506 c("--mzdecimal"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	507 type = "integer",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	508 default = DEFAULT_MZDECIMAL,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	509 action = "store",
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	510 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	511 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	512 "Number of decimal to write for MZ"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	513 ),
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	514 metavar = "number"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	515 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	516 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	517 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	518 c("--r_threshold"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	519 type = "integer",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	520 default = DEFAULT_R_THRESHOLD,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	521 action = "store",
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	522 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	523 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	524 "R-Pearson correlation threshold between precursor and fragment",
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	525 "absolute intensity"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	526 ),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	527 metavar = "number"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	528 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	529 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	530 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	531 c("--min_number_scan"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	532 type = "numeric",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	533 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	534 default = DEFAULT_MINNUMBERSCAN,
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	535 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	536 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	537 "Fragments are kept if there are found in a minimum number",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	538 "of min_number_scan scans"
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	539 ),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	540 metavar = "number"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	541 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	542 return(parser)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	543 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	544
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	545 stop_with_status <- function(msg, status) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	546 message(sprintf("Error: %s", msg))
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	547 message(sprintf("Error code: %s", status))
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	548 base::quit(status = status)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	549 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	550
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	551 check_args_validity <- function(args) { ## nolint cyclocomp_linter
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	552 sysvars <- Sys.getenv()
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	553 sysvarnames <- names(sysvars)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	554 if (length(args$output) == 0 \|\| nchar(args$output[1]) == 0) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	555 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	556 "Missing output parameters. Please set it with --output.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	557 MISSING_PARAMETER_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	558 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	559 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	560 if (length(args$precursors) == 0 \|\| nchar(args$precursors[1]) == 0) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	561 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	562 "Missing precursors parameters. Please set it with --precursors.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	563 MISSING_PARAMETER_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	564 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	565 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	566 if (length(args$fragments) == 0 \|\| nchar(args$fragments[1]) == 0) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	567 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	568 "Missing fragments parameters. Please set it with --fragments.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	569 MISSING_PARAMETER_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	570 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	571 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	572 if (length(args$compounds) == 0 \|\| nchar(args$compounds[1]) == 0) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	573 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	574 "Missing compounds parameters. Please set it with --compounds.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	575 MISSING_PARAMETER_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	576 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	577 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	578 if (!file.exists(args$precursors)) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	579 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	580 sprintf(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	581 "Precursors file %s does not exist or cannot be accessed.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	582 args$precursors
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	583 ),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	584 MISSING_INPUT_FILE_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	585 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	586 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	587 if (!file.exists(args$fragments)) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	588 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	589 sprintf(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	590 "Fragments file %s does not exist or cannot be accessed.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	591 args$fragments
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	592 ),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	593 MISSING_INPUT_FILE_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	594 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	595 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	596 if (!file.exists(args$compounds)) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	597 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	598 sprintf(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	599 "Compounds file %s does not exist or cannot be accessed.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	600 args$compounds
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	601 ),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	602 MISSING_INPUT_FILE_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	603 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	604 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	605 if (
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	606 "_GALAXY_JOB_HOME_DIR" %in% sysvarnames
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	607 \|\| "_GALAXY_JOB_TMP_DIR" %in% sysvarnames
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	608 \|\| "GALAXY_MEMORY_MB" %in% sysvarnames
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	609 \|\| "GALAXY_MEMORY_MB_PER_SLOT" %in% sysvarnames
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	610 \|\| "GALAXY_SLOTS" %in% sysvarnames
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	611 ) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	612 check_galaxy_args_validity(args)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	613 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	614 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	615
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	616 check_galaxy_args_validity <- function(args) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	617 if (!file.exists(args$output)) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	618 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	619 sprintf(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	620 "Output file %s does not exist or cannot be accessed.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	621 args$output
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	622 ),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	623 MISSING_INPUT_FILE_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	624 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	625 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	626 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	627
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	628 main <- function(args) {
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	629 if (args$version) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	630 cat(sprintf("%s\n", MS2SNOOP_VERSION))
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	631 base::quit(status = 0)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	632 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	633 sessionInfo()
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	634 check_args_validity(args)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	635 if (args$debug) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	636 set_debug()
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	637 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	638 if (args$verbose) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	639 set_verbose()
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	640 }
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	641 ## MSpurity precursors file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	642 precursors <- read.table(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	643 file = args$precursors,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	644 header = TRUE,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	645 sep = "\t",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	646 quote = "\""
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	647 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	648 ## MSpurity fragments file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	649 fragments <- read.table(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	650 file = args$fragments,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	651 header = TRUE,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	652 sep = "\t",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	653 quote = "\""
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	654 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	655 ## list of compounds : col1=Name of molecule, col2=m/z, col3=retention time
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	656 compounds <- read.table(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	657 file = args$compounds,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	658 sep = "\t",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	659 quote = "\"",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	660 header = TRUE
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	661 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	662
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	663 res_all <- NULL
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	664 for (i in seq_len(nrow(compounds))) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	665 ## loop execution for all compounds in the compounds file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	666 res_cor <- NULL
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	667 res_cor <- extract_fragments(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	668 precursors = precursors,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	669 fragments = fragments,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	670 mzref = compounds[[2]][i],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	671 rtref = compounds[[3]][i],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	672 c_name = compounds[[1]][i],
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	673 min_number_scan = args$min_number_scan,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	674 mzdecimal = args$mzdecimal,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	675 r_threshold = args$r_threshold,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	676 seuil_ra = args$seuil_ra,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	677 tolmz = args$tolmz,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	678 tolrt = args$tolrt
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	679 )
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	680 if (!is.null(res_cor)) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	681 if (is.null(res_all)) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	682 res_all <- res_cor
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	683 } else {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	684 res_all <- rbind(res_all, res_cor)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	685 }
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	686 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	687 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	688
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	689 if (is.null(res_all)) {
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	690 stop_with_status("No result at all!", NO_ANY_RESULT_ERROR)
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	691 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	692 write.table(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	693 x = res_all,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	694 file = args$output,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	695 sep = "\t",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	696 row.names = FALSE
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	697 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	698 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	699
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	700 unset_debug()
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	701 unset_verbose()
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	702 args <- optparse::parse_args(create_parser())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	703 main(args)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	704
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	705 warnings()

Mercurial > repos > workflow4metabolomics > ms2snoop

annotate MS2snoop.R @ 2:a35fde23940e draft