diff picard_CollectHsMetrics.xml @ 33:3f254c5ced1d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8

--- a/picard_CollectHsMetrics.xml	Mon Sep 25 08:32:17 2023 +0000
+++ b/picard_CollectHsMetrics.xml	Sun Mar 03 16:06:11 2024 +0000
@@ -1,5 +1,4 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool name="CollectHsMetrics" id="picard_CollectHsMetrics" version="@TOOL_VERSION@">
+<tool name="CollectHsMetrics" id="picard_CollectHsMetrics" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>compute metrics about datasets generated through hybrid-selection (e.g. exome)</description>
     <macros>
         <import>picard_macros.xml</import>
@@ -9,19 +8,18 @@
 @java_options@
 @symlink_element_identifier@
 
-picard
-CollectHsMetrics
-INPUT='$escaped_element_identifier'
-OUTPUT='${outFile}'
-MINIMUM_MAPPING_QUALITY=${minimum_mapping_quality}
-MINIMUM_BASE_QUALITY=${minimum_base_quality}
-COVERAGE_CAP=${coverage_cap}
-CLIP_OVERLAPPING_READS=${clip_overlapping_reads}
-BAIT_INTERVALS='${baitFile}'
-TARGET_INTERVALS='${targetFile}'
-VALIDATION_STRINGENCY=${validation_stringency}
-QUIET=true
-VERBOSITY=ERROR
+picard CollectHsMetrics
+--INPUT '$escaped_element_identifier'
+--OUTPUT '${outFile}'
+--MINIMUM_MAPPING_QUALITY ${minimum_mapping_quality}
+--MINIMUM_BASE_QUALITY ${minimum_base_quality}
+--COVERAGE_CAP ${coverage_cap}
+--CLIP_OVERLAPPING_READS ${clip_overlapping_reads}
+--BAIT_INTERVALS '${baitFile}'
+--TARGET_INTERVALS '${targetFile}'
+--VALIDATION_STRINGENCY ${validation_stringency}
+--QUIET true
+--VERBOSITY ERROR
     ]]></command>
     <inputs>
         <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />