# HG changeset patch
# User iuc
# Date 1539704920 14400
# Node ID d837223d4ad2df8b1801162013c14167a241393d
# Parent a5a13ea16d17d5bcd7f733a98fe2717f75e8fa72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 78c3dea7dcd0c854fe7e6dc1d2b2349956167661
diff -r a5a13ea16d17 -r d837223d4ad2 picard_EstimateLibraryComplexity.xml
--- a/picard_EstimateLibraryComplexity.xml Tue Jun 19 11:28:30 2018 -0400
+++ b/picard_EstimateLibraryComplexity.xml Tue Oct 16 11:48:40 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="${validation_stringency}"
@@ -36,10 +35,7 @@
-
-
-
-
+
diff -r a5a13ea16d17 -r d837223d4ad2 picard_MarkDuplicates.xml
--- a/picard_MarkDuplicates.xml Tue Jun 19 11:28:30 2018 -0400
+++ b/picard_MarkDuplicates.xml Tue Oct 16 11:48:40 2018 -0400
@@ -24,9 +24,8 @@
DUPLICATE_SCORING_STRATEGY='${duplicate_scoring_strategy}'
- #import pipes
#if $read_name_regex:
- READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) }
+ READ_NAME_REGEX='${ str( $read_name_regex ) }'
#end if
OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}'
@@ -55,11 +54,7 @@
-
-
-
-
-
+
diff -r a5a13ea16d17 -r d837223d4ad2 picard_MarkDuplicatesWithMateCigar.xml
--- 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 @@
-
-
-
-
+
diff -r a5a13ea16d17 -r d837223d4ad2 picard_macros.xml
--- a/picard_macros.xml Tue Jun 19 11:28:30 2018 -0400
+++ b/picard_macros.xml Tue Oct 16 11:48:40 2018 -0400
@@ -9,6 +9,17 @@
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2.18.2