# HG changeset patch
# User lecorguille
# Date 1541794360 18000
# Node ID a9d451591d7bcd16994fc51e88df8137a70bf19c
# Parent  ca6e35ab34874ea133afc89fe5e056db83942b1e
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989

diff -r ca6e35ab3487 -r a9d451591d7b lib.r
--- a/lib.r	Tue Oct 09 04:38:19 2018 -0400
+++ b/lib.r	Fri Nov 09 15:12:40 2018 -0500
@@ -198,6 +198,9 @@
     variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
     dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
 
+    # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
+    variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
+
     write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
     write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
 
@@ -260,9 +263,9 @@
     #Create the sampleMetada dataframe
     sampleMetadata <- xdata@phenoData@data
     rownames(sampleMetadata) <- NULL
-    colnames(sampleMetadata) <-  c("sampleMetadata", "class")
+    colnames(sampleMetadata) <-  c("sample_name", "class")
 
-    sampleNamesOrigin <- sampleMetadata$sampleMetadata
+    sampleNamesOrigin <- sampleMetadata$sample_name
     sampleNamesMakeNames <- make.names(sampleNamesOrigin)
 
     if (any(duplicated(sampleNamesMakeNames))) {
@@ -280,7 +283,7 @@
         }
     }
 
-    sampleMetadata$sampleMetadata <- sampleNamesMakeNames
+    sampleMetadata$sample_name <- sampleNamesMakeNames
 
 
     #For each sample file, the following actions are done
diff -r ca6e35ab3487 -r a9d451591d7b repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Oct 09 04:38:19 2018 -0400
+++ b/repository_dependencies.xml	Fri Nov 09 15:12:40 2018 -0500
@@ -1,5 +1,5 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <repositories>
-    <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
-	<repository changeset_revision="544f6d2329ac" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
-</repositories>
+    <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    <repository changeset_revision="544f6d2329ac" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu"/>
+</repositories>
\ No newline at end of file
diff -r ca6e35ab3487 -r a9d451591d7b test-data/noclass.merged.sampleMetadata.tsv
--- a/test-data/noclass.merged.sampleMetadata.tsv	Tue Oct 09 04:38:19 2018 -0400
+++ b/test-data/noclass.merged.sampleMetadata.tsv	Fri Nov 09 15:12:40 2018 -0500
@@ -1,4 +1,4 @@
-sampleMetadata	class
+sample_name	class
 ko15	.
 ko16	.
 wt15	.