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comparison picard_ValidateSamFile.xml @ 30:b502c227b5e6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 0244aa33464cc27d1ce881cb310b8eda36e9a89c
author iuc
date Mon, 22 Aug 2022 09:56:00 +0000
parents 881d7645d1bf
children f9242e01365a
comparison
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29:1aac2a13842a 30:b502c227b5e6
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@">1</token> 5 <token name="@WRAPPER_VERSION@">2</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>
43 43
44 MAX_OUTPUT="${max_output}" 44 MAX_OUTPUT="${max_output}"
45 REFERENCE_SEQUENCE="${reference_fasta_filename}" 45 REFERENCE_SEQUENCE="${reference_fasta_filename}"
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 VALIDATE_INDEX="${validate_index}"
48 MAX_OPEN_TEMP_FILES=`ulimit -Sn` 49 MAX_OPEN_TEMP_FILES=`ulimit -Sn`
49 50
50 VERBOSITY=ERROR 51 VERBOSITY=ERROR
51 @TMPDIR_OPTION@ 52 @TMPDIR_OPTION@
52 QUIET=true 53 QUIET=true