Mercurial > repos > devteam > picard
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
| author | iuc |
|---|---|
| date | Sun, 03 Mar 2024 16:06:11 +0000 |
| parents | f9242e01365a |
| children |
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--- 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" />