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

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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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32:f9242e01365a 33:3f254c5ced1d
1 <?xml version="1.0" encoding="UTF-8"?> 1 <tool name="CollectHsMetrics" id="picard_CollectHsMetrics" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <tool name="CollectHsMetrics" id="picard_CollectHsMetrics" version="@TOOL_VERSION@">
3 <description>compute metrics about datasets generated through hybrid-selection (e.g. exome)</description> 2 <description>compute metrics about datasets generated through hybrid-selection (e.g. exome)</description>
4 <macros> 3 <macros>
5 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
6 </macros> 5 </macros>
7 <expand macro="requirements" /> 6 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
9 @java_options@ 8 @java_options@
10 @symlink_element_identifier@ 9 @symlink_element_identifier@
11 10
12 picard 11 picard CollectHsMetrics
13 CollectHsMetrics 12 --INPUT '$escaped_element_identifier'
14 INPUT='$escaped_element_identifier' 13 --OUTPUT '${outFile}'
15 OUTPUT='${outFile}' 14 --MINIMUM_MAPPING_QUALITY ${minimum_mapping_quality}
16 MINIMUM_MAPPING_QUALITY=${minimum_mapping_quality} 15 --MINIMUM_BASE_QUALITY ${minimum_base_quality}
17 MINIMUM_BASE_QUALITY=${minimum_base_quality} 16 --COVERAGE_CAP ${coverage_cap}
18 COVERAGE_CAP=${coverage_cap} 17 --CLIP_OVERLAPPING_READS ${clip_overlapping_reads}
19 CLIP_OVERLAPPING_READS=${clip_overlapping_reads} 18 --BAIT_INTERVALS '${baitFile}'
20 BAIT_INTERVALS='${baitFile}' 19 --TARGET_INTERVALS '${targetFile}'
21 TARGET_INTERVALS='${targetFile}' 20 --VALIDATION_STRINGENCY ${validation_stringency}
22 VALIDATION_STRINGENCY=${validation_stringency} 21 --QUIET true
23 QUIET=true 22 --VERBOSITY ERROR
24 VERBOSITY=ERROR
25 ]]></command> 23 ]]></command>
26 <inputs> 24 <inputs>
27 <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" /> 25 <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" />
28 <param name="baitFile" type="data" format="picard_interval_list" label="An interval list file that contains the locations of the baits used" help="If empty, upload or convert from BED" /> 26 <param name="baitFile" type="data" format="picard_interval_list" label="An interval list file that contains the locations of the baits used" help="If empty, upload or convert from BED" />
29 <param name="targetFile" type="data" format="picard_interval_list" label="An interval list file that contains the locations of the targets" help="If empty, upload or convert from BED" /> 27 <param name="targetFile" type="data" format="picard_interval_list" label="An interval list file that contains the locations of the targets" help="If empty, upload or convert from BED" />