From 63f81e2a308080779a0b85c978639085701399fa Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 19 Aug 2022 13:47:59 +0200
Subject: [PATCH] picard: implement missing parameters

---
 tools/picard/picard_CollectSequencingArtifactsMetrics.xml | 5 +++--
 tools/picard/picard_ValidateSamFile.xml                   | 3 ++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/tools/picard/picard_CollectSequencingArtifactsMetrics.xml b/tools/picard/picard_CollectSequencingArtifactsMetrics.xml
index baeb6dad4f1..ed5373abf54 100644
--- a/tools/picard/picard_CollectSequencingArtifactsMetrics.xml
+++ b/tools/picard/picard_CollectSequencingArtifactsMetrics.xml
@@ -2,7 +2,7 @@
   <description>Collect metrics to quantify single-base sequencing artifacts</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
+    <token name="@WRAPPER_VERSION@">2</token>
   </macros>
   <expand macro="requirements">
     <requirement type="package" version="3.4.1">r-base</requirement>
@@ -31,7 +31,8 @@
     INCLUDE_UNPAIRED='${unpaired}'
     MAXIMUM_INSERT_SIZE='${max_size}'
     MINIMUM_INSERT_SIZE='${min_size}'
-    MINIMUM_MAPPING_QUALITY='${minim_map_quality}';
+    MINIMUM_MAPPING_QUALITY='${minim_map_quality}'
+    VALIDATION_STRINGENCY='${validation_stringency}';
   ]]></command>  
   <inputs>
     <param name='inputFile' format="sam,bam" type='data' label='SAM/BAM Input file'/>
diff --git a/tools/picard/picard_ValidateSamFile.xml b/tools/picard/picard_ValidateSamFile.xml
index 9cbfe246870..221d4401cc6 100644
--- a/tools/picard/picard_ValidateSamFile.xml
+++ b/tools/picard/picard_ValidateSamFile.xml
@@ -2,7 +2,7 @@
   <description>assess validity of SAM/BAM dataset</description>
   <macros>
     <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
+    <token name="@WRAPPER_VERSION@">2</token>
   </macros>
   <expand macro="requirements" />
   <stdio>
@@ -45,6 +45,7 @@
     REFERENCE_SEQUENCE="${reference_fasta_filename}"
     IGNORE_WARNINGS="${ignore_warnings}"
     IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"
+    VALIDATE_INDEX="${validate_index}"
     MAX_OPEN_TEMP_FILES=`ulimit -Sn`
 
     VERBOSITY=ERROR