diff picard_MarkDuplicates.xml @ 19:5053a18d9bc8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73

--- a/picard_MarkDuplicates.xml	Sat Jan 20 08:28:24 2018 -0500
+++ b/picard_MarkDuplicates.xml	Mon Apr 16 21:27:29 2018 -0400
@@ -1,7 +1,8 @@
-<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.2">
+<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
   <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
   <macros>
     <import>picard_macros.xml</import>
+    <token name="@WRAPPER_VERSION@">0</token>
   </macros>
   <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
@@ -53,7 +54,7 @@
     </param>
 
     <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default='' (uses : separation)">
- 
+
       <sanitizer>
         <valid initial="string.printable">
         </valid>
@@ -127,7 +128,7 @@
                                 colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be
                                 tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements
                                 are assumed to be tile, x and y values.  Default value: ''
-                                
+
 
   DUPLICATE_SCORING_STRATEGY=ScoringStrategy
   DS=ScoringStrategy            The scoring strategy for choosing the non-duplicate among candidates.  Default value:
@@ -136,7 +137,7 @@
   OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer
                                 The maximum offset between two duplicate clusters in order to consider them optical
                                 duplicates. This should be set to 100 for (circa 2011+) read names and typical flowcells.
-                                Structured flow cells (NovaSeq, HiSeq 4000, X) should use ~2500. 
+                                Structured flow cells (NovaSeq, HiSeq 4000, X) should use ~2500.
                                 For older conventions, distances could be to some fairly small number (e.g. 5-10 pixels)
                                 Default value: 100.
 
@@ -145,6 +146,5 @@
 @more_info@
 
   </help>
+  <expand macro="citations" />
 </tool>
-
-