# HG changeset patch
# User lecorguille
# Date 1486742593 18000
# Node ID a6938c381d4e669ea0d7dee0cbec6c2e92919b08
# Parent  99094333f540d80277f62d7017f540aa7037f222
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4

diff -r 99094333f540 -r a6938c381d4e README.rst
--- a/README.rst	Thu Feb 09 04:51:18 2017 -0500
+++ b/README.rst	Fri Feb 10 11:03:13 2017 -0500
@@ -2,12 +2,10 @@
 Changelog/News
 --------------
 
-**Version 2.1.1 - 07/02/2017**
+**Version 2.1.0 - 07/02/2017**
 
 - IMPROVEMENT: change the management of the peaklist ids. The main ids remain the same as xcms generated. The export setiings now only add custom names in the variableMetadata tab (namecustom)
 
-**Version 2.1.0 - 03/02/2017**
-
 - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data
 
 **Version 2.0.8 - 22/12/2016**
diff -r 99094333f540 -r a6938c381d4e abims_xcms_fillPeaks.xml
--- a/abims_xcms_fillPeaks.xml	Thu Feb 09 04:51:18 2017 -0500
+++ b/abims_xcms_fillPeaks.xml	Fri Feb 10 11:03:13 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.1.1">
+<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.1.0">
 
     <description>Integrate a sample's signal in regions where peak groups are not represented to create new peaks in missing areas</description>
 
@@ -12,9 +12,9 @@
     <command><![CDATA[
         @COMMAND_XCMS_SCRIPT@
         xfunction fillPeaks
-        image $image
+        image '$image'
 
-        xsetRdataOutput $xsetRData
+        xsetRdataOutput '$xsetRData'
 
         method $method
 
@@ -272,12 +272,10 @@
 Changelog/News
 --------------
 
-**Version 2.1.1 - 07/02/2017**
+**Version 2.1.0 - 07/02/2017**
 
 - IMPROVEMENT: change the management of the peaklist ids. The main ids remain the same as xcms generated. The export setiings now only add custom names in the variableMetadata tab (namecustom)
 
-**Version 2.1.0 - 03/02/2017**
-
 - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data
 
 **Version 2.0.8 - 22/12/2016**
diff -r 99094333f540 -r a6938c381d4e macros.xml
--- a/macros.xml	Thu Feb 09 04:51:18 2017 -0500
+++ b/macros.xml	Fri Feb 10 11:03:13 2017 -0500
@@ -25,8 +25,8 @@
     <token name="@COMMAND_LOG_EXIT@">
         ;
         return=\$?;
-        mv log.txt $log;
-        cat $log;
+        mv log.txt '$log';
+        cat '$log';
         sh -c "exit \$return"
     </token>
 
@@ -35,12 +35,12 @@
     <token name="@COMMAND_FILE_LOAD@">
         #if $file_load_conditional.file_load_select == "yes":
             #if $file_load_conditional.inputs.input == "zip_file":
-                zipfile $file_load_conditional.inputs.zip_file
+                zipfile '$file_load_conditional.inputs.zip_file'
             #else
                 #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_conditional.inputs.single_file ] )
                 #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_conditional.inputs.single_file ] )
 
-                singlefile_galaxyPath $singlefile_galaxyPath singlefile_sampleName $singlefile_sampleName
+                singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
             #end if
         #end if
     </token>
@@ -72,8 +72,8 @@
 
     <token name="@COMMAND_PEAKLIST@">
         #if $peaklist.peaklistBool
-            variableMetadataOutput $variableMetadata
-            dataMatrixOutput $dataMatrix
+            variableMetadataOutput '$variableMetadata'
+            dataMatrixOutput '$dataMatrix'
             convertRTMinute $peaklist.convertRTMinute
             numDigitsMZ $peaklist.numDigitsMZ
             numDigitsRT $peaklist.numDigitsRT