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comparison picard_ValidateSamFile.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 e65f2d5fd3d8
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14:486d7500da69 15:a5a13ea16d17
1 <tool name="ValidateSamFile" id="picard_ValidateSamFile" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="ValidateSamFile" id="picard_ValidateSamFile" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>assess validity of SAM/BAM dataset</description> 2 <description>assess validity of SAM/BAM dataset</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 <stdio> 8 <stdio>
9 <exit_code range="1:" level="warning"/> 9 <exit_code range="1:" level="warning"/>
10 </stdio> 10 </stdio>
46 IGNORE_WARNINGS="${ignore_warnings}" 46 IGNORE_WARNINGS="${ignore_warnings}"
47 IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}" 47 IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"
48 MAX_OPEN_TEMP_FILES=`ulimit -Sn` 48 MAX_OPEN_TEMP_FILES=`ulimit -Sn`
49 49
50 VERBOSITY=ERROR 50 VERBOSITY=ERROR
51 @TMPDIR_OPTION@
51 QUIET=true 52 QUIET=true
52 53
53 ]]></command> 54 ]]></command>
54 <inputs> 55 <inputs>
55 <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset." /> 56 <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset." />