ms2snoop: MS2snoop.R annotate

annotate MS2snoop.R @ 4:856001213966 draft

planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715

author	workflow4metabolomics
date	Wed, 06 Jul 2022 10:38:39 +0000
parents	c68c94865667
children	78d5a12406c2

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
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	18 assign("MS2SNOOP_VERSION", "2.0.0")
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,
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	90 c_name,
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	91 inchikey,
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	92 elemcomposition
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	93 ) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	94 ## du fait de la difference de nombre de colonne entre la dataframe qui
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	95 ## inclue les scans en 1ere col, mzRef se decale de 1
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	96 refcol <- refcol - 1
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	97 ## compute relative intensities max=100%
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	98 rel_int <- sum_int[-1]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	99 rel_int <- rel_int / max(rel_int)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	100
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	101 ## define max value on vertical axis (need to increase in order to plot the
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	102 ## label of fragments)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	103 ymax <- max(rel_int) + 0.2 * max(rel_int)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	104
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	105 par(mfrow = c(2, 1))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	106 plot(vmz, rel_int, type = "h", ylim = c(0, ymax), main = c_name)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	107 ## low correl coef. will be display in grey
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	108 cor_low <- which(round(cor_abs_int, 2) < r_threshold)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	109
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	110 lbmzcor <- sprintf("%s(r=%s)", vmz, round(cor_abs_int, 2))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	111
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	112 if (length(cor_low) > 0) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	113 text(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	114 vmz[cor_low],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	115 rel_int[cor_low],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	116 lbmzcor[cor_low],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	117 cex = 0.5,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	118 col = "grey",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	119 srt = 90,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	120 adj = 0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	121 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	122 if (length(vmz) - length(cor_low) > 1) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	123 text(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	124 vmz[-c(refcol, cor_low)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	125 rel_int[-c(refcol, cor_low)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	126 lbmzcor[-c(refcol, cor_low)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	127 cex = 0.6,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	128 col = 1,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	129 srt = 90,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	130 adj = 0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	131 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	132 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	133 } else {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	134 if (length(vmz) > 1) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	135 text(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	136 vmz[-c(refcol)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	137 rel_int[-c(refcol)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	138 lbmzcor[-c(refcol)],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	139 cex = 0.6,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	140 col = 1,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	141 srt = 90,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	142 adj = 0
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 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	146
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	147 text(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	148 vmz[refcol],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	149 rel_int[refcol],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	150 lbmzcor[refcol],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	151 cex = 0.8,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	152 col = 2,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	153 srt = 90,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	154 adj = 0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	155 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	156
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	157 ## prepare result file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	158 corValid <- (round(cor_abs_int, 2) >= r_threshold) ##nolint object_name_linter
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	159 cp_res <- data.frame(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	160 rep(c_name, length(vmz)),
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	161 rep(inchikey, length(vmz)),
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	162 rep(elemcomposition, length(vmz)),
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	163 rep(fid, length(vmz)),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	164 vmz,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	165 cor_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	166 sum_int[-1],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	167 rel_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	168 corValid
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	169 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	170
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	171 colnames(cp_res) <- c(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	172 "compoundName",
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	173 "inchikey",
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	174 "elemcomposition",
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	175 "fileid",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	176 "fragments_mz",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	177 "CorWithPrecursor",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	178 "AbsoluteIntensity",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	179 "relativeIntensity",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	180 "corValid"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	181 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	182 return(cp_res)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	183
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	184 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	185
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	186 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	187 #' @title extract_fragments
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	188 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	189 #' @param precursors the precursor list from mspurity
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	190 #' @param fragments the fragments list from ms purity
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	191 #' @param mzref
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	192 #' @param rtref
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	193 #' @param c_name
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	194 #' @param r_threshold default = DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	195 #' @param seuil_ra default = DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	196 #' @param tolmz default = DEFAULT_EXTRACT_FRAGMENTS_TOLMZ
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	197 #' @param tolrt default = DEFAULT_EXTRACT_FRAGMENTS_TOLRT
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	198 #' @returns
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	199 #'
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	200 #' @description
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	201 #' function for extraction of fragments corresponding to precursors
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	202 #' detected by MSPurity
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	203 extract_fragments <- function( ## nolint cyclocomp_linter
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	204 precursors,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	205 fragments,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	206 mzref,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	207 rtref,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	208 c_name,
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	209 inchikey,
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	210 elemcomposition,
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	211 min_number_scan,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	212 mzdecimal,
3 c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	213 r_threshold = DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD,
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	214 seuil_ra = DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA,
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	215 tolmz = DEFAULT_EXTRACT_FRAGMENTS_TOLMZ,
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	216 tolrt = DEFAULT_EXTRACT_FRAGMENTS_TOLRT
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	217 ) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	218 ## filter precursor in the precursors file based on mz and rt in the
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	219 ## compound list
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	220 cat("processing ", c_name, "\n")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	221 selected_precursors <- which(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	222 (abs(precursors$precurMtchMZ - mzref) <= tolmz)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	223 & (abs(precursors$precurMtchRT - rtref) <= tolrt)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	224 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	225
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	226 ## check if there is the precursor in the file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	227 if (length(selected_precursors) > 0) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	228
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	229 sprecini <- precursors[selected_precursors, ]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	230
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	231 ## check if fragments corresponding to precursor are found in several
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	232 ## files (collision energy)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	233 ## this lead to a processing for each fileid
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	234 mf <- levels(as.factor(sprecini$fileid))
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	235 if (length(mf) > 1 && global_verbose) {
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	236 cat(" several files detected for this compounds :\n")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	237 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	238
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	239 for (f in seq_along(mf)) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	240
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	241 sprec <- sprecini[sprecini$fileid == mf[f], ]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	242
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	243 ## selection of fragment in the fragments file with the grpid common in
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	244 ## both fragments and precursors
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	245 selfrgt <- levels(as.factor(sprec$grpid))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	246 sfrgt <- fragments[
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	247 fragments$grpid %in% selfrgt
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	248 & fragments$fileid == mf[f],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	249 ]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	250
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	251 ## filter fragments on relative intensity seuil_ra = user defined
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	252 ## parameter (MSpurity flags could be used here)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	253 sfrgtfil <- sfrgt[sfrgt$ra > seuil_ra, ]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	254
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	255 mznominal <- round(x = sfrgtfil$mz, mzdecimal)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	256 sfrgtfil <- data.frame(sfrgtfil, mznominal)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	257
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	258 ## creation of cross table row=scan col=mz X=ra
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	259 vmz <- levels(as.factor(sfrgtfil$mznominal))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	260
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	261 if (global_verbose) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	262 cat(" fragments :", vmz)
3 c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	263 cat("\n")
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	264 }
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	265
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	266 ## mz of precursor in data precursor to check correlation with
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	267 mz_prec <- paste0("mz", round(mean(sprec$mz), mzdecimal))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	268
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	269 for (m in seq_along(vmz)) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	270
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	271 ## absolute intensity
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	272 cln <- c(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	273 which(colnames(sfrgtfil) == "acquisitionNum"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	274 which(colnames(sfrgtfil) == "i")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	275 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	276 int_mz <- sfrgtfil[sfrgtfil$mznominal == vmz[m], cln]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	277 colnames(int_mz)[2] <- paste0("mz", vmz[m])
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	278
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	279 ## average intensities of mass in duplicate scans
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	280 comp_scans <- aggregate(x = int_mz, by = list(int_mz[[1]]), FUN = mean)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	281 int_mz <- comp_scans[, -1]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	282
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	283 if (m == 1) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	284 ds_abs_int <- int_mz
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	285 } else {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	286 ds_abs_int <- merge(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	287 x = ds_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	288 y = int_mz,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	289 by.x = 1,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	290 by.y = 1,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	291 all.x = TRUE,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	292 all.y = TRUE
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	293 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	294 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	295 }
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	296 if (global_debug) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	297 print(ds_abs_int)
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	298 write.table(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	299 x = ds_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	300 file = paste0(c_name, "ds_abs_int.txt"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	301 row.names = FALSE,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	302 sep = "\t"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	303 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	304 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	305
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	306 ## elimination of mz with less than min_number_scan scans (user defined
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	307 ## parameter)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	308 xmz <- rep(NA, ncol(ds_abs_int) - 1)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	309 sum_int <- rep(NA, ncol(ds_abs_int))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	310 nbxmz <- 0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	311 nb_scan_check <- min(nrow(ds_abs_int), min_number_scan)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	312
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	313 for (j in 2:ncol(ds_abs_int)) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	314 sum_int[j] <- sum(ds_abs_int[j], na.rm = TRUE)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	315 if (sum(!is.na(ds_abs_int[[j]])) < nb_scan_check) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	316 nbxmz <- nbxmz + 1
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	317 xmz[nbxmz] <- j
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
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	321 xmz <- xmz[-which(is.na(xmz))]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	322 if (length(xmz) > 0) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	323 ds_abs_int <- ds_abs_int[, -c(xmz)]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	324 sum_int <- sum_int[-c(xmz)]
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	325 ## liste des mz keeped decale de 1 avec ds_abs_int
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	326 vmz <- as.numeric(vmz[-c(xmz - 1)])
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	327 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	328
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	329 ## reference ion for correlation computing = precursor OR maximum
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	330 ## intensity ion in precursor is not present
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	331 refcol <- which(colnames(ds_abs_int) == mz_prec)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	332 if (length(refcol) == 0) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	333 refcol <- which(sum_int == max(sum_int, na.rm = TRUE))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	334 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	335 pdf(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	336 file = sprintf("%s_processing_file%s.pdf", c_name, mf[f]),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	337 width = 8,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	338 height = 11
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	339 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	340 par(mfrow = c(3, 2))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	341
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	342 ## Pearson correlations between absolute intensities computing
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	343 cor_abs_int <- rep(NA, length(vmz))
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	344
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	345 if (length(refcol) > 0) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	346 for (i in 2:length(ds_abs_int)) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	347 cor_abs_int[i - 1] <- cor(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	348 x = ds_abs_int[[refcol]],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	349 y = ds_abs_int[[i]],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	350 use = "pairwise.complete.obs",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	351 method = "pearson"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	352 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	353 plot(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	354 ds_abs_int[[refcol]],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	355 ds_abs_int[[i]],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	356 xlab = colnames(ds_abs_int)[refcol],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	357 ylab = colnames(ds_abs_int)[i],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	358 main = sprintf(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	359 "%s corr coeff r=%s", c_name, round(cor_abs_int[i - 1], 2)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	360 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	361 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	362 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	363 ## plot pseudo spectra
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	364 res_comp_by_file <- plot_pseudo_spectra(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	365 x = ds_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	366 r_threshold = r_threshold,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	367 fid = mf[f],
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	368 sum_int = sum_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	369 vmz = vmz,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	370 cor_abs_int = cor_abs_int,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	371 refcol = refcol,
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	372 c_name = c_name,
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	373 inchikey = inchikey,
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	374 elemcomposition = elemcomposition
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	375 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	376 if (f == 1) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	377 res_comp <- res_comp_by_file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	378 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	379 } else {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	380 res_comp_by_file <- NULL
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	381 cat(" non detected in fragments file \n")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	382 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	383 if (!is.null(res_comp_by_file)) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	384 res_comp <- rbind(res_comp, res_comp_by_file)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	385 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	386 dev.off()
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	387 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	388 } else {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	389 res_comp <- NULL
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	390 cat(" non detected in precursor file \n")
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	391 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	392 return(res_comp)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	393 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	394
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	395 set_global <- function(var, value) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	396 assign(var, value, envir = globalenv())
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_debug <- function() {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	400 set_global("global_debug", 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_debug <- function() {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	404 set_global("global_debug", FALSE)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	405 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	406
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	407 set_verbose <- function() {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	408 set_global("global_verbose", TRUE)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	409 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	410
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	411 unset_verbose <- function() {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	412 set_global("global_verbose", FALSE)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	413 }
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	414
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	415 create_parser <- function() {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	416 parser <- optparse::OptionParser()
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	417 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	418 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	419 c("-v", "--verbose"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	420 action = "store_true",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	421 default = FALSE,
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	422 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	423 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	424 "Print extra output"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	425 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	426 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	427 parser <- optparse::add_option(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	428 parser,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	429 c("-V", "--version"),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	430 action = "store_true",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	431 default = FALSE,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	432 help = "Prints version and exits"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	433 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	434 parser <- optparse::add_option(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	435 parser,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	436 c("-d", "--debug"),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	437 action = "store_true",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	438 default = FALSE,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	439 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	440 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	441 "Print debug outputs"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	442 )
0 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("-o", "--output"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	447 type = "character",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	448 default = DEFAULT_OUTPUT_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 output 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("-p", "--precursors"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	455 type = "character",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	456 default = DEFAULT_PRECURSOR_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 precursors 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("-f", "--fragments"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	463 type = "character",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	464 default = DEFAULT_FRAGMENTS_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 fragments 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("-c", "--compounds"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	471 type = "character",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	472 default = DEFAULT_COMPOUNDS_PATH,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	473 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	474 help = "Path to the compounds file [default %default]"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	475 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	476 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	477 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	478 c("--tolmz"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	479 type = "numeric",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	480 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	481 default = DEFAULT_TOLMZ,
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	482 metavar = "number",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	483 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	484 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	485 "Tolerance for MZ (in Dalton) to match the standard in the compounds"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	486 )
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	487 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	488 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	489 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	490 c("--tolrt"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	491 type = "integer",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	492 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	493 default = DEFAULT_TOLRT,
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	494 metavar = "number",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	495 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	496 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	497 "RT (in seconds) to match the standard in the compounds"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	498 )
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	499 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	500 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	501 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	502 c("--seuil_ra"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	503 type = "numeric",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	504 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	505 default = DEFAULT_SEUIL_RA,
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	506 metavar = "number",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	507 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	508 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	509 "relative intensity threshold"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	510 ),
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	511 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	512 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	513 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	514 c("--mzdecimal"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	515 type = "integer",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	516 default = DEFAULT_MZDECIMAL,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	517 action = "store",
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	518 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	519 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	520 "Number of decimal to write for MZ"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	521 ),
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	522 metavar = "number"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	523 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	524 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	525 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	526 c("--r_threshold"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	527 type = "integer",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	528 default = DEFAULT_R_THRESHOLD,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	529 action = "store",
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	530 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	531 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	532 "R-Pearson correlation threshold between precursor and fragment",
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	533 "absolute intensity"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	534 ),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	535 metavar = "number"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	536 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	537 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	538 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	539 c("--min_number_scan"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	540 type = "numeric",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	541 action = "store",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	542 default = DEFAULT_MINNUMBERSCAN,
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	543 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	544 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	545 "Fragments are kept if there are found in a minimum number",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	546 "of min_number_scan scans"
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	547 ),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	548 metavar = "number"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	549 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	550 return(parser)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	551 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	552
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	553 stop_with_status <- function(msg, status) {
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	554 sink(stderr())
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	555 message(sprintf("Error: %s", msg))
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	556 message(sprintf("Error code: %s", status))
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	557 sink(NULL)
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	558 base::quit(status = status)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	559 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	560
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	561 check_args_validity <- function(args) { ## nolint cyclocomp_linter
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	562 sysvars <- Sys.getenv()
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	563 sysvarnames <- names(sysvars)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	564 if (length(args$output) == 0 \|\| nchar(args$output[1]) == 0) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	565 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	566 "Missing output parameters. Please set it with --output.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	567 MISSING_PARAMETER_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	568 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	569 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	570 if (length(args$precursors) == 0 \|\| nchar(args$precursors[1]) == 0) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	571 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	572 "Missing precursors parameters. Please set it with --precursors.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	573 MISSING_PARAMETER_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	574 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	575 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	576 if (length(args$fragments) == 0 \|\| nchar(args$fragments[1]) == 0) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	577 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	578 "Missing fragments parameters. Please set it with --fragments.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	579 MISSING_PARAMETER_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	580 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	581 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	582 if (length(args$compounds) == 0 \|\| nchar(args$compounds[1]) == 0) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	583 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	584 "Missing compounds parameters. Please set it with --compounds.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	585 MISSING_PARAMETER_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	586 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	587 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	588 if (!file.exists(args$precursors)) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	589 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	590 sprintf(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	591 "Precursors file %s does not exist or cannot be accessed.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	592 args$precursors
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	593 ),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	594 MISSING_INPUT_FILE_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	595 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	596 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	597 if (!file.exists(args$fragments)) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	598 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	599 sprintf(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	600 "Fragments file %s does not exist or cannot be accessed.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	601 args$fragments
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	602 ),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	603 MISSING_INPUT_FILE_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	604 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	605 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	606 if (!file.exists(args$compounds)) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	607 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	608 sprintf(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	609 "Compounds file %s does not exist or cannot be accessed.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	610 args$compounds
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	611 ),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	612 MISSING_INPUT_FILE_ERROR
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 if (
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	616 "_GALAXY_JOB_HOME_DIR" %in% sysvarnames
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	617 \|\| "_GALAXY_JOB_TMP_DIR" %in% sysvarnames
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	618 \|\| "GALAXY_MEMORY_MB" %in% sysvarnames
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	619 \|\| "GALAXY_MEMORY_MB_PER_SLOT" %in% sysvarnames
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	620 \|\| "GALAXY_SLOTS" %in% sysvarnames
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	621 ) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	622 check_galaxy_args_validity(args)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	623 }
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 check_galaxy_args_validity <- function(args) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	627 if (!file.exists(args$output)) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	628 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	629 sprintf(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	630 "Output file %s does not exist or cannot be accessed.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	631 args$output
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	632 ),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	633 MISSING_INPUT_FILE_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	634 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	635 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	636 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	637
3 c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	638 get_csv_or_tsv <- function(
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	639 path,
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	640 sep_stack = c("\t", ",", ";"),
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	641 header = TRUE,
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	642 quote = "\""
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	643 ) {
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	644 sep <- sep_stack[1]
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	645 result <- tryCatch({
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	646 read.table(
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	647 file = path,
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	648 sep = sep,
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	649 header = header,
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	650 quote = quote
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	651 )
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	652 }, error = function(e) {
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	653 return(data.frame())
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	654 })
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	655 if (length(sep_stack) == 1) {
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	656 return(result)
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	657 }
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	658 # if (
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	659 # ncol(result) == 0 \|\| ## failed
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	660 # ncol(result) == 1 ## only one row, suspicious, possible fail # nolint
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	661 # ) {
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	662 new_result <- get_csv_or_tsv(
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	663 path,
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	664 sep_stack = sep_stack[-1],
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	665 header = header,
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	666 quote = quote
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	667 )
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	668 if (ncol(new_result) > ncol(result)) {
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	669 return(new_result)
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	670 }
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	671 # }
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	672 return(result)
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	673 }
c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	674
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	675 uniformize_columns <- function(df) {
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	676 cols <- colnames(df)
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	677 for (func in c(tolower)) {
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	678 cols <- func(cols)
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	679 }
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	680 colnames(df) <- cols
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	681 return(df)
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	682 }
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	683
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	684 main <- function(args) {
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	685 if (args$version) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	686 cat(sprintf("%s\n", MS2SNOOP_VERSION))
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	687 base::quit(status = 0)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	688 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	689 sessionInfo()
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	690 check_args_validity(args)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	691 if (args$debug) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	692 set_debug()
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	693 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	694 if (args$verbose) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	695 set_verbose()
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	696 }
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	697 ## MSpurity precursors file
3 c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	698 precursors <- get_csv_or_tsv(args$precursors)
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	699 ## MSpurity fragments file
3 c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	700 fragments <- get_csv_or_tsv(args$fragments)
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	701 ## list of compounds : col1=Name of molecule, col2=m/z, col3=retention time
3 c68c94865667 planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0 workflow4metabolomics parents: 1 diff changeset	702 compounds <- get_csv_or_tsv(args$compounds)
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	703
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	704 compounds <- uniformize_columns(compounds)
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	705 mandatory_columns <- c(
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	706 "compound_name",
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	707 "mz",
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	708 "rtsec",
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	709 "inchikey"
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	710 )
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	711 presents <- mandatory_columns %in% colnames(compounds)
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	712 if (!all(presents)) {
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	713 stop_with_status(
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	714 sprintf(
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	715 "Some columns are missing: %s",
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	716 paste(mandatory_columns[which(!presents)], collapse = ", ")
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	717 ),
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	718 BAD_PARAMETER_VALUE_ERROR
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	719 )
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	720 }
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	721
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	722 res_all <- NULL
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	723 for (i in seq_len(nrow(compounds))) {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	724 ## loop execution for all compounds in the compounds file
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	725 res_cor <- NULL
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	726 res_cor <- extract_fragments(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	727 precursors = precursors,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	728 fragments = fragments,
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	729 mzref = compounds[["mz"]][i],
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	730 rtref = compounds[["rtsec"]][i],
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	731 c_name = compounds[["compound_name"]][i],
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	732 inchikey = compounds[["inchikey"]][i],
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	733 elemcomposition = compounds[["elemcomposition"]][i],
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	734 min_number_scan = args$min_number_scan,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	735 mzdecimal = args$mzdecimal,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	736 r_threshold = args$r_threshold,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	737 seuil_ra = args$seuil_ra,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	738 tolmz = args$tolmz,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	739 tolrt = args$tolrt
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	740 )
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	741 if (!is.null(res_cor)) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	742 if (is.null(res_all)) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	743 res_all <- res_cor
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	744 } else {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	745 res_all <- rbind(res_all, res_cor)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	746 }
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	747 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	748 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	749
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	750 if (is.null(res_all)) {
1 df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43 workflow4metabolomics parents: 0 diff changeset	751 stop_with_status("No result at all!", NO_ANY_RESULT_ERROR)
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	752 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	753 write.table(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	754 x = res_all,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	755 file = args$output,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	756 sep = "\t",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	757 row.names = FALSE
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	758 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	759 }
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	760
4 856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	761 global_debug <- FALSE
856001213966 planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 workflow4metabolomics parents: 3 diff changeset	762 global_verbose <- FALSE
0 91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	763 args <- optparse::parse_args(create_parser())
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	764 main(args)
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	765
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032" workflow4metabolomics parents: diff changeset	766 warnings()

Mercurial > repos > workflow4metabolomics > ms2snoop

annotate MS2snoop.R @ 4:856001213966 draft