# HG changeset patch
# User lecorguille
# Date 1486742481 18000
# Node ID 329cfa3d2be63e393e27e296abe8a29847e6d6bc
# Parent  25938ab94950aaf3f3020d6e94c182de06e54fc6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4

diff -r 25938ab94950 -r 329cfa3d2be6 abims_xcms_xcmsSet.xml
--- a/abims_xcms_xcmsSet.xml	Thu Feb 09 04:49:34 2017 -0500
+++ b/abims_xcms_xcmsSet.xml	Fri Feb 10 11:01:21 2017 -0500
@@ -12,17 +12,17 @@
         @COMMAND_XCMS_SCRIPT@
 
         #if $inputs.input == "zip_file":
-            zipfile $inputs.zip_file
+            zipfile '$inputs.zip_file'
         #elif $inputs.input == "single_file":
-            singlefile_galaxyPath $inputs.single_file singlefile_sampleName $inputs.single_file.name
+            singlefile_galaxyPath '$inputs.single_file' singlefile_sampleName '$inputs.single_file.name'
         #end if
 
         xfunction xcmsSet
 
-        xsetRdataOutput $xsetRData
-        sampleMetadataOutput $sampleMetadata
-        ticspdf $ticsRawPdf
-        bicspdf $bpcsRawPdf
+        xsetRdataOutput '$xsetRData'
+        sampleMetadataOutput '$sampleMetadata'
+        ticspdf '$ticsRawPdf'
+        bicspdf '$bpcsRawPdf'
 
 
         #if $options_scanrange.option == "show":
diff -r 25938ab94950 -r 329cfa3d2be6 macros.xml
--- a/macros.xml	Thu Feb 09 04:49:34 2017 -0500
+++ b/macros.xml	Fri Feb 10 11:01:21 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