diff picard_MarkDuplicatesWithMateCigar.xml @ 16:d837223d4ad2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 78c3dea7dcd0c854fe7e6dc1d2b2349956167661

--- a/picard_MarkDuplicatesWithMateCigar.xml	Tue Jun 19 11:28:30 2018 -0400
+++ b/picard_MarkDuplicatesWithMateCigar.xml	Tue Oct 16 11:48:40 2018 -0400
@@ -26,8 +26,7 @@
 
     DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}"
 
-    #import pipes
-    READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
+    READ_NAME_REGEX='${ str( $read_name_regex ) }'
     OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"
 
 
@@ -54,10 +53,7 @@
 
 
     <param name="read_name_regex" type="text" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse 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=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.">
-      <sanitizer>
-        <valid initial="string.printable">
-        </valid>
-      </sanitizer>
+      <expand macro="sanitize_query" />
     </param>
     <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>