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comparison picard_CollectSequencingArtifactsMetrics.xml @ 26:fc3866ddc7b6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 0244aa33464cc27d1ce881cb310b8eda36e9a89c
author iuc
date Mon, 22 Aug 2022 09:54:37 +0000
parents f8748e3fd865
children
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25:3b55709c0a01 26:fc3866ddc7b6
1 <tool id='picard_artifact_metrics' name='Picard Collect Sequencing Artifact Metrics' version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool id='picard_artifact_metrics' name='Picard Collect Sequencing Artifact Metrics' version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>Collect metrics to quantify single-base sequencing artifacts</description> 2 <description>Collect metrics to quantify single-base sequencing artifacts</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 <token name="@WRAPPER_VERSION@">1</token> 5 <token name="@WRAPPER_VERSION@">2</token>
6 </macros> 6 </macros>
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <requirement type="package" version="3.4.1">r-base</requirement> 8 <requirement type="package" version="3.4.1">r-base</requirement>
9 </expand> 9 </expand>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
29 #end if; 29 #end if;
30 MINIMUM_QUALITY_SCORE='${min_quality_score}' 30 MINIMUM_QUALITY_SCORE='${min_quality_score}'
31 INCLUDE_UNPAIRED='${unpaired}' 31 INCLUDE_UNPAIRED='${unpaired}'
32 MAXIMUM_INSERT_SIZE='${max_size}' 32 MAXIMUM_INSERT_SIZE='${max_size}'
33 MINIMUM_INSERT_SIZE='${min_size}' 33 MINIMUM_INSERT_SIZE='${min_size}'
34 MINIMUM_MAPPING_QUALITY='${minim_map_quality}'; 34 MINIMUM_MAPPING_QUALITY='${minim_map_quality}'
35 VALIDATION_STRINGENCY='${validation_stringency}';
35 ]]></command> 36 ]]></command>
36 <inputs> 37 <inputs>
37 <param name='inputFile' format="sam,bam" type='data' label='SAM/BAM Input file'/> 38 <param name='inputFile' format="sam,bam" type='data' label='SAM/BAM Input file'/>
38 <conditional name="reference_source"> 39 <conditional name="reference_source">
39 <param name="reference_source_selector" type="select" label="Load reference genome from"> 40 <param name="reference_source_selector" type="select" label="Load reference genome from">