# HG changeset patch
# User lecorguille
# Date 1538663782 14400
# Node ID 7bb43bf0b54696ffd29822dd40ff8306635df6a9
# Parent  4c25647cd4df7290463d2a2586e5830cb15b3752
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty

diff -r 4c25647cd4df -r 7bb43bf0b546 lib.r
--- a/lib.r	Wed Sep 19 02:53:07 2018 -0400
+++ b/lib.r	Thu Oct 04 10:36:22 2018 -0400
@@ -186,9 +186,9 @@
 
 #@author G. Le Corguille
 # value: intensity values to be used into, maxo or intb
-getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput) {
+getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
     dataMatrix <- featureValues(xdata, method="medret", value=intval)
-    colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
+    colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
     dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
     variableMetadata <- featureDefinitions(xdata)
     colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"