diff picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml @ 13:7e6fd3d0f16e draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e

--- a/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml	Sun Nov 27 15:11:50 2016 -0500
+++ b/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml	Tue Dec 06 10:04:41 2016 -0500
@@ -6,21 +6,20 @@
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
-    
     picard
     RevertOriginalBaseQualitiesAndAddMateCigar
-    
-    INPUT="${inputFile}"
+
+    INPUT='$inputFile'
     OUTPUT="${outFile}"
-    
+
     RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}"
     MAX_RECORDS_TO_EXAMINE="${max_records_to_examine}"
-    
+
     SORT_ORDER=coordinate
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-  
+
   ]]></command>
   <inputs>
     <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
@@ -28,13 +27,13 @@
     <param name="max_records_to_examine" type="integer" value="10000" min="0" label="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the dataset" help="MAX_RECORDS_TO_EXAMINE; default=10,000"/>
 
     <expand macro="VS" />
-    
-  </inputs> 
-  
+
+  </inputs>
+
   <outputs>
     <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/>
@@ -44,8 +43,8 @@
       <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
-  
-  
+
+
   <help>
 
 **Purpose**
@@ -57,11 +56,11 @@
 @description@
 
   RESTORE_ORIGINAL_QUALITIES=Boolean
-  OQ=Boolean                    True to restore original qualities from the OQ field to the QUAL field if available.  
-                                Default value: true. Possible values: {true, false} 
-  
-  MAX_RECORDS_TO_EXAMINE=IntegerThe maximum number of records to examine to determine if we can exit early and not 
-                                output, given that there are a no original base qualities (if we are to restore) and mate 
+  OQ=Boolean                    True to restore original qualities from the OQ field to the QUAL field if available.
+                                Default value: true. Possible values: {true, false}
+
+  MAX_RECORDS_TO_EXAMINE=IntegerThe maximum number of records to examine to determine if we can exit early and not
+                                output, given that there are a no original base qualities (if we are to restore) and mate
                                 cigars exist. Set to 0 to never skip the file.  Default value: 10000.
 
 @more_info@