Mercurial > repos > devteam > picard
comparison picard_FixMateInformation.xml @ 15:a5a13ea16d17 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
author | iuc |
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date | Tue, 19 Jun 2018 11:28:30 -0400 |
parents | 486d7500da69 |
children | c943f4a04af0 |
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14:486d7500da69 | 15:a5a13ea16d17 |
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1 <tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> | 1 <tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> |
2 <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description> | 2 <description>ensure that all mate-pair information is in sync between each read and it's mate pair</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 picard | 10 picard |
16 | 16 |
17 SORT_ORDER=coordinate | 17 SORT_ORDER=coordinate |
18 VALIDATION_STRINGENCY="${validation_stringency}" | 18 VALIDATION_STRINGENCY="${validation_stringency}" |
19 QUIET=true | 19 QUIET=true |
20 VERBOSITY=ERROR | 20 VERBOSITY=ERROR |
21 @TMPDIR_OPTION@ | |
21 | 22 |
22 ]]></command> | 23 ]]></command> |
23 <inputs> | 24 <inputs> |
24 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> | 25 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> |
25 <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/> | 26 <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/> |