Mercurial > repos > lecorguille > xcms_summary

diff 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
line wrap: on
line diff
--- a/xcms_summary.r	Wed Feb 12 08:30:41 2020 -0500
+++ b/xcms_summary.r	Tue May 12 16:39:28 2020 -0400
@@ -67,18 +67,22 @@
 if (!is.null(args$user_email)) user_email = args$user_email;
 
 # if the RData come from XCMS 1.x
-if (exists("xset")) xobject <- xset
-# retrocompatability
-if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(sampnames(xobject)))
+if (exists("xset")) {
+    xobject <- xset
+    # retrocompatability
+    if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(sampnames(xobject)))
+}
 # if the RData come from CAMERA
 if (exists("xa")) xobject <- xa@xcmsSet
 # if the RData come from XCMS 3.x
-if (exists("xdata")) xobject <- xdata
+if (exists("xdata")) {
+    xobject <- xdata
+    if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(xdata@phenoData@data$sample_name))
+}
 
 if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.")
 
 
-
 # ----- MAIN PROCESSING INFO -----
 writehtml("<!DOCTYPE html>")
 writehtml("<HTML lang='en'>")