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comparison picard_MarkDuplicatesWithMateCigar.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 6f9c0884a3e7
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19:5053a18d9bc8 20:2a17c789e0a5
1 <tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>examine aligned records in BAM datasets to locate duplicate molecules</description> 2 <description>examine aligned records in BAM datasets to locate duplicate molecules</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@
33 33
34 BLOCK_SIZE=100000 34 BLOCK_SIZE=100000
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="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="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 name="comment" type="text" label="Add this comment to BAM dataset"/> 43 <param name="comment" type="text" label="Add this comment to BAM dataset"/>