Mercurial > repos > lecorguille > xcms_summary

comparison xcms_summary.r @ 26:db6549f27ad1 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8"
author workflow4metabolomics
date Tue, 12 May 2020 16:39:28 -0400
parents 46be2c523a7f
children bed23aa27b4b
comparison
equal deleted inserted replaced
25:acc66e5c23d7 26:db6549f27ad1
65 65
66 user_email <- NULL 66 user_email <- NULL
67 if (!is.null(args$user_email)) user_email = args$user_email; 67 if (!is.null(args$user_email)) user_email = args$user_email;
68 68
69 # if the RData come from XCMS 1.x 69 # if the RData come from XCMS 1.x
70 if (exists("xset")) xobject <- xset 70 if (exists("xset")) {
71 # retrocompatability 71 xobject <- xset
72 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(sampnames(xobject))) 72 # retrocompatability
73 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(sampnames(xobject)))
74 }
73 # if the RData come from CAMERA 75 # if the RData come from CAMERA
74 if (exists("xa")) xobject <- xa@xcmsSet 76 if (exists("xa")) xobject <- xa@xcmsSet
75 # if the RData come from XCMS 3.x 77 # if the RData come from XCMS 3.x
76 if (exists("xdata")) xobject <- xdata 78 if (exists("xdata")) {
79 xobject <- xdata
80 if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(xdata@phenoData@data$sample_name))
81 }
77 82
78 if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.") 83 if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.")
79
80 84
81 85
82 # ----- MAIN PROCESSING INFO ----- 86 # ----- MAIN PROCESSING INFO -----
83 writehtml("<!DOCTYPE html>") 87 writehtml("<!DOCTYPE html>")
84 writehtml("<HTML lang='en'>") 88 writehtml("<HTML lang='en'>")