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comparison picard_MarkDuplicates.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 d837223d4ad2
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14:486d7500da69 15:a5a13ea16d17
1 <tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="MarkDuplicates" id="picard_MarkDuplicates" 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@
36 #end if 36 #end if
37 37
38 VALIDATION_STRINGENCY='${validation_stringency}' 38 VALIDATION_STRINGENCY='${validation_stringency}'
39 QUIET=true 39 QUIET=true
40 VERBOSITY=ERROR 40 VERBOSITY=ERROR
41 @TMPDIR_OPTION@
41 42
42 ]]></command> 43 ]]></command>
43 <inputs> 44 <inputs>
44 <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"/> 45 <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"/>
45 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments"> 46 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">