diff picard_MergeSamFiles.xml @ 13:7e6fd3d0f16e draft

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

--- a/picard_MergeSamFiles.xml	Sun Nov 27 15:11:50 2016 -0500
+++ b/picard_MergeSamFiles.xml	Tue Dec 06 10:04:41 2016 -0500
@@ -6,17 +6,16 @@
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
-    
     picard
     MergeSamFiles
-    
+
     #for $element in $inputFile:
       INPUT="${element}"
     #end for
-    
+
     OUTPUT="${outFile}"
     MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}"
-    
+
     ASSUME_SORTED="${assume_sorted}"
     #for $element in $comments:
       COMMENT="${element.comment}"
@@ -27,7 +26,7 @@
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-  
+
   ]]></command>
   <inputs>
     <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
@@ -37,15 +36,15 @@
     <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
       <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
     </repeat>
-    
+
     <expand macro="VS" />
-    
-  </inputs> 
-  
+
+  </inputs>
+
   <outputs>
     <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Merged BAM dataset"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/>
@@ -55,8 +54,8 @@
       <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
-  
-  
+
+
   <help>
 
 **Purpose**
@@ -68,17 +67,17 @@
 @description@
 
   ASSUME_SORTED=Boolean
-  AS=Boolean                    If true, assume that the input files are in the same sort order as the requested output 
-                                sort order, even if their headers say otherwise.  Default value: false. This option can 
-                                be set to 'null' to clear the default value. Possible values: {true, false} 
-  
+  AS=Boolean                    If true, assume that the input files are in the same sort order as the requested output
+                                sort order, even if their headers say otherwise.  Default value: false. This option can
+                                be set to 'null' to clear the default value. Possible values: {true, false}
+
   MERGE_SEQUENCE_DICTIONARIES=Boolean
-  MSD=Boolean                   Merge the sequence dictionaries  Default value: false. This option can be set to 'null' 
-                                to clear the default value. Possible values: {true, false} 
-  
+  MSD=Boolean                   Merge the sequence dictionaries  Default value: false. This option can be set to 'null'
+                                to clear the default value. Possible values: {true, false}
+
   COMMENT=String
-  CO=String                     Comment(s) to include in the merged output file's header.  This option may be specified 0 
-                                or more times. 
+  CO=String                     Comment(s) to include in the merged output file's header.  This option may be specified 0
+                                or more times.
 
 
 @more_info@