# HG changeset patch
# User lecorguille
# Date 1541794475 18000
# Node ID 7a19925478e8d63a02673041bb25fd3a966d7d5a
# Parent  95e689b7f27f7b3873fb6dc44067b5233e357608
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989

diff -r 95e689b7f27f -r 7a19925478e8 README.rst
--- a/README.rst	Tue Oct 09 04:39:40 2018 -0400
+++ b/README.rst	Fri Nov 09 15:14:35 2018 -0500
@@ -2,6 +2,10 @@
 Changelog/News
 --------------
 
+**Version 3.0.0.1 - 09/11/2018**
+
+- BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist
+
 **Version 3.0.0.0 - 08/03/2018**
 
 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.
diff -r 95e689b7f27f -r 7a19925478e8 abims_xcms_group.xml
--- a/abims_xcms_group.xml	Tue Oct 09 04:39:40 2018 -0400
+++ b/abims_xcms_group.xml	Fri Nov 09 15:14:35 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@WRAPPER_VERSION@.0">
+<tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@WRAPPER_VERSION@.1">
 
     <description>Perform the correspondence, the grouping of chromatographic peaks within and between samples.</description>
 
@@ -355,6 +355,10 @@
 Changelog/News
 --------------
 
+**Version 3.0.0.1 - 09/11/2018**
+
+- BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist
+
 **Version 3.0.0.0 - 08/03/2018**
 
 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.
diff -r 95e689b7f27f -r 7a19925478e8 lib.r
--- a/lib.r	Tue Oct 09 04:39:40 2018 -0400
+++ b/lib.r	Fri Nov 09 15:14:35 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 95e689b7f27f -r 7a19925478e8 repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Oct 09 04:39:40 2018 -0400
+++ b/repository_dependencies.xml	Fri Nov 09 15:14:35 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>
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