--- a/picard_EstimateLibraryComplexity.xml	Tue Jun 19 11:28:49 2018 -0400
+++ b/picard_EstimateLibraryComplexity.xml	Tue Oct 16 11:49:10 2018 -0400
@@ -18,8 +18,7 @@
     MAX_DIFF_RATE="${max_diff_rate}"
     MIN_MEAN_QUALITY="${min_mean_quality}"
     MAX_GROUP_RATIO="${max_group_ratio}"
-    #import pipes
-    READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
+    READ_NAME_REGEX='${ str( $read_name_regex ) }'
     OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"
 
     VALIDATION_STRINGENCY="${validation_stringency}"
@@ -36,10 +35,7 @@
     <param name="max_group_ratio" type="integer" value="500" label="Do not process self-similar groups that are this many times over the mean expected group size" help="MAX_GROUP_RATIO; I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then the mean expected group size would be approximately 10 reads; default-500"/>
 
     <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"/>