# HG changeset patch
# User lecorguille
# Date 1486742610 18000
# Node ID abb66f65f1aff49378041ff00205b81de1a3d019
# Parent  c3646d3f175025d0d105f51bbf6b8ea71d304668
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4

diff -r c3646d3f1750 -r abb66f65f1af abims_xcms_summary.xml
--- a/abims_xcms_summary.xml	Thu Feb 09 04:51:36 2017 -0500
+++ b/abims_xcms_summary.xml	Fri Feb 10 11:03:30 2017 -0500
@@ -16,8 +16,8 @@
     <command><![CDATA[
         $__tool_directory__/xcms_summary.r
 
-        image $image
-        htmlOutput $htmlOutput
+        image '$image'
+        htmlOutput '$htmlOutput'
         user_email $__user_email__
 
     ]]></command>
diff -r c3646d3f1750 -r abb66f65f1af macros.xml
--- a/macros.xml	Thu Feb 09 04:51:36 2017 -0500
+++ b/macros.xml	Fri Feb 10 11:03:30 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