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comparison picard_CollectAlignmentSummaryMetrics.xml @ 20:2a17c789e0a5 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 11:28:49 -0400
parents 5053a18d9bc8
children 585027e65f3b
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equal deleted inserted replaced
19:5053a18d9bc8 20:2a17c789e0a5
1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>writes a file containing summary alignment metrics</description> 2 <description>writes a file containing summary alignment metrics</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 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @java_options@ 9 @java_options@
10 @symlink_element_identifier@ 10 @symlink_element_identifier@
32 ASSUME_SORTED="${assume_sorted}" 32 ASSUME_SORTED="${assume_sorted}"
33 33
34 VALIDATION_STRINGENCY="${validation_stringency}" 34 VALIDATION_STRINGENCY="${validation_stringency}"
35 QUIET=true 35 QUIET=true
36 VERBOSITY=ERROR 36 VERBOSITY=ERROR
37 @TMPDIR_OPTION@
37 38
38 ]]></command> 39 ]]></command>
39 <inputs> 40 <inputs>
40 <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."/> 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."/>
41 <conditional name="reference_source"> 42 <conditional name="reference_source">