diff picard_RevertSam.xml @ 13:7e6fd3d0f16e draft

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

--- a/picard_RevertSam.xml	Sun Nov 27 15:11:50 2016 -0500
+++ b/picard_RevertSam.xml	Tue Dec 06 10:04:41 2016 -0500
@@ -6,31 +6,30 @@
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
-    
     picard
     RevertSam
-    
-    INPUT="${inputFile}"
+
+    INPUT='$inputFile'
     OUTPUT="${outFile}"
-    
+
     RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}"
     REMOVE_DUPLICATE_INFORMATION="${remove_duplicate_information}"
     REMOVE_ALIGNMENT_INFORMATION="${remove_alignment_information}"
-     
+
     #for $attribute_to_clear in $attributes_to_clear:
       ATTRIBUTE_TO_CLEAR="${attribute_to_clear.attribute}"
     #end for
-    
+
     SANITIZE="${sanitize}"
     MAX_DISCARD_FRACTION="${max_discard_fraction}"
     SAMPLE_ALIAS="${sample_alias}"
     LIBRARY_NAME="${library_name}"
-    
+
     SORT_ORDER="${sort_order}"
     VALIDATION_STRINGENCY="${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"/>
@@ -50,13 +49,13 @@
       <option value="unsorted">Unsorted</option>
     </param>
     <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_RevertSam.bam" ftype="bam"/>
@@ -73,8 +72,8 @@
       <output name="outFile" file="picard_RevertSam_test1.bam" ftype="bam" lines_diff="4"/>
     </test>
   </tests>
-  
-  
+
+
   <help>
 
 **Purpose**
@@ -85,46 +84,46 @@
 
 @description@
 
-  SORT_ORDER=SortOrder  
+  SORT_ORDER=SortOrder
   SO=SortOrder                  The sort order to create the reverted output file with.  Default value: queryname.
-                                Possible values: {unsorted, queryname, coordinate} 
-  
+                                Possible values: {unsorted, queryname, coordinate}
+
   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} 
-  
+  OQ=Boolean                    True to restore original qualities from the OQ field to the QUAL field if available.
+                                Default value: true. Possible values: {true, false}
+
   REMOVE_DUPLICATE_INFORMATION=Boolean
-                                Remove duplicate read flags from all reads.  Note that if this is true and 
-                                REMOVE_ALIGNMENT_INFORMATION==false,  the output may have the unusual but sometimes 
-                                desirable trait of having unmapped reads that are marked as duplicates.  Default value: 
-                                true. Possible values: {true, false} 
-  
+                                Remove duplicate read flags from all reads.  Note that if this is true and
+                                REMOVE_ALIGNMENT_INFORMATION==false,  the output may have the unusual but sometimes
+                                desirable trait of having unmapped reads that are marked as duplicates.  Default value:
+                                true. Possible values: {true, false}
+
   REMOVE_ALIGNMENT_INFORMATION=Boolean
-                                Remove all alignment information from the file.  Default value: true. TPossible values: {true, false} 
-  
-  ATTRIBUTE_TO_CLEAR=String     When removing alignment information, the set of optional tags to remove.  This option may 
-                                be specified 0 or more times. 
-  
-  SANITIZE=Boolean              WARNING: This option is potentially destructive. If enabled will discard reads in order 
-                                to produce a consistent output BAM. Reads discarded include (but are not limited to) 
-                                paired reads with missing mates, duplicated records, records with mismatches in length of 
-                                bases and qualities. This option can only be enabled if the output sort order is 
-                                queryname and will always cause sorting to occur.  Possible values: {true, false} 
-  
-  MAX_DISCARD_FRACTION=Double   If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to 
-                                sanitization thenthe program will exit with an Exception instead of exiting cleanly. 
-                                Output BAM will still be valid.  Default value: 0.01. 
-  
+                                Remove all alignment information from the file.  Default value: true. TPossible values: {true, false}
+
+  ATTRIBUTE_TO_CLEAR=String     When removing alignment information, the set of optional tags to remove.  This option may
+                                be specified 0 or more times.
+
+  SANITIZE=Boolean              WARNING: This option is potentially destructive. If enabled will discard reads in order
+                                to produce a consistent output BAM. Reads discarded include (but are not limited to)
+                                paired reads with missing mates, duplicated records, records with mismatches in length of
+                                bases and qualities. This option can only be enabled if the output sort order is
+                                queryname and will always cause sorting to occur.  Possible values: {true, false}
+
+  MAX_DISCARD_FRACTION=Double   If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to
+                                sanitization thenthe program will exit with an Exception instead of exiting cleanly.
+                                Output BAM will still be valid.  Default value: 0.01.
+
   SAMPLE_ALIAS=String
-  ALIAS=String                  The sample alias to use in the reverted output file.  This will override the existing 
-                                sample alias in the file and is used only if all the read groups in the input file have 
-                                the same sample alias   Default value: null. 
-  
+  ALIAS=String                  The sample alias to use in the reverted output file.  This will override the existing
+                                sample alias in the file and is used only if all the read groups in the input file have
+                                the same sample alias   Default value: null.
+
   LIBRARY_NAME=String
-  LIB=String                    The library name to use in the reverted output file.  This will override the existing 
-                                sample alias in the file and is used only if all the read groups in the input file have 
-                                the same sample alias   Default value: null. 
-  
+  LIB=String                    The library name to use in the reverted output file.  This will override the existing
+                                sample alias in the file and is used only if all the read groups in the input file have
+                                the same sample alias   Default value: null.
+
 @more_info@
 
   </help>