# HG changeset patch
# User lecorguille
# Date 1486742558 18000
# Node ID 51b9f9452794f9d20cd8e2b29f0d4ed5156c40c8
# Parent  08768644f9c43e6bf6825d1f549e7fae5f8feb23
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4

diff -r 08768644f9c4 -r 51b9f9452794 abims_xcms_retcor.xml
--- a/abims_xcms_retcor.xml	Thu Feb 09 04:50:45 2017 -0500
+++ b/abims_xcms_retcor.xml	Fri Feb 10 11:02:38 2017 -0500
@@ -11,13 +11,13 @@
 
     <command><![CDATA[
         @COMMAND_XCMS_SCRIPT@
-        image $image
+        image '$image'
         xfunction retcor
 
-        xsetRdataOutput $xsetRData
-        ticspdf $ticsCorPdf
-        bicspdf $bpcsCorPdf
-        rplotspdf $rplotsPdf
+        xsetRdataOutput '$xsetRData'
+        ticspdf '$ticsCorPdf'
+        bicspdf '$bpcsCorPdf'
+        rplotspdf '$rplotsPdf'
 
         method $methods.method
         #if $methods.method == "obiwarp":
diff -r 08768644f9c4 -r 51b9f9452794 macros.xml
--- a/macros.xml	Thu Feb 09 04:50:45 2017 -0500
+++ b/macros.xml	Fri Feb 10 11:02:38 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