# HG changeset patch
# User lecorguille
# Date 1538660775 14400
# Node ID 19d6e8ecbccb64c773e8f43d49343bed42adb0cd
# Parent  9bfe06bed015b2a620d997c2d5983d374e8b8341
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty

diff -r 9bfe06bed015 -r 19d6e8ecbccb lib.r
--- a/lib.r	Wed Sep 19 09:33:43 2018 -0400
+++ b/lib.r	Thu Oct 04 09:46:15 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"
diff -r 9bfe06bed015 -r 19d6e8ecbccb repository_dependencies.xml
--- a/repository_dependencies.xml	Wed Sep 19 09:33:43 2018 -0400
+++ b/repository_dependencies.xml	Thu Oct 04 09:46:15 2018 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
 <repositories>
-    <repository changeset_revision="91815b6d07fe" name="no_unzip_datatype" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="fcc646bbf366" name="no_unzip_datatype" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 	<repository changeset_revision="8ce71291b600" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>