diff picard_FixMateInformation.xml @ 13:7e6fd3d0f16e draft

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

--- a/picard_FixMateInformation.xml	Sun Nov 27 15:11:50 2016 -0500
+++ b/picard_FixMateInformation.xml	Tue Dec 06 10:04:41 2016 -0500
@@ -6,33 +6,32 @@
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
-    
     picard
     FixMateInformation
     INPUT="${inputFile}"
     OUTPUT="${outFile}"
     ASSUME_SORTED=${assume_sorted}
     ADD_MATE_CIGAR=${add_mate_cigar}
-    
+
     SORT_ORDER=coordinate
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-  
+
   ]]></command>
   <inputs>
     <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
     <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
     <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/>
- 
+
     <expand macro="VS" />
-    
-  </inputs> 
-  
+
+  </inputs>
+
   <outputs>
     <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/>
@@ -42,8 +41,8 @@
       <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
-  
-  
+
+
   <help>
 
 **Purpose**
@@ -64,12 +63,12 @@
 @description@
 
   ASSUME_SORTED=Boolean
-  AS=Boolean                    If true, assume that the input file is queryname sorted, even if the header says 
-                                otherwise.  Default value: false. 
-  
+  AS=Boolean                    If true, assume that the input file is queryname sorted, even if the header says
+                                otherwise.  Default value: false.
+
   ADD_MATE_CIGAR=Boolean
-  MC=Boolean                    Adds the mate CIGAR tag (MC) if true, does not if false.  Default value: true. 
-  
+  MC=Boolean                    Adds the mate CIGAR tag (MC) if true, does not if false.  Default value: true.
+
 @more_info@
 
   </help>