Mercurial > repos > devteam > picard
comparison picard_ValidateSamFile.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 | e65f2d5fd3d8 |
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14:486d7500da69 | 15:a5a13ea16d17 |
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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." /> |