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comparison picard_CleanSam.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 f9242e01365a
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19:5053a18d9bc8 20:2a17c789e0a5
1 <tool id="picard_CleanSam" name="CleanSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool id="picard_CleanSam" name="CleanSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>perform SAM/BAM grooming</description> 2 <description>perform SAM/BAM grooming</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@
12 CleanSam 12 CleanSam
13 INPUT='$escaped_element_identifier' 13 INPUT='$escaped_element_identifier'
14 OUTPUT="${outFile}" 14 OUTPUT="${outFile}"
15 QUIET=true 15 QUIET=true
16 VERBOSITY=ERROR 16 VERBOSITY=ERROR
17 @TMPDIR_OPTION@
17 VALIDATION_STRINGENCY=${validation_stringency} 18 VALIDATION_STRINGENCY=${validation_stringency}
18 ]]></command> 19 ]]></command>
19 20
20 <inputs> 21 <inputs>
21 <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"/> 22 <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"/>