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comparison picard_CollectInsertSizeMetrics.xml @ 15:a5a13ea16d17 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
author iuc
date Tue, 19 Jun 2018 11:28:30 -0400
parents 486d7500da69
children fdca9493e09b
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14:486d7500da69 15:a5a13ea16d17
1 <tool name="CollectInsertSizeMetrics" id="picard_CollectInsertSizeMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="CollectInsertSizeMetrics" id="picard_CollectInsertSizeMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>plots distribution of insert sizes</description> 2 <description>plots distribution of insert sizes</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 <token name="@WRAPPER_VERSION@">0</token> 5 <token name="@WRAPPER_VERSION@">1</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[
33 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" 33 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
34 34
35 VALIDATION_STRINGENCY="${validation_stringency}" 35 VALIDATION_STRINGENCY="${validation_stringency}"
36 QUIET=true 36 QUIET=true
37 VERBOSITY=ERROR 37 VERBOSITY=ERROR
38 @TMPDIR_OPTION@
38 39
39 ]]></command> 40 ]]></command>
40 <inputs> 41 <inputs>
41 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/> 42 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
42 <conditional name="reference_source"> 43 <conditional name="reference_source">