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comparison picard_MergeBamAlignment.xml @ 20:2a17c789e0a5 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 11:28:49 -0400
parents 5053a18d9bc8
children 585027e65f3b
comparison
equal deleted inserted replaced
19:5053a18d9bc8 20:2a17c789e0a5
1 <tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>merge alignment data with additional info stored in an unmapped BAM dataset</description> 2 <description>merge alignment data with additional info stored in an unmapped 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 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @java_options@ 9 @java_options@
10 #set $picard_dict = "localref.dict" 10 #set $picard_dict = "localref.dict"
15 #if str( $reference_source.reference_source_selector ) == "history": 15 #if str( $reference_source.reference_source_selector ) == "history":
16 16
17 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" 17 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
18 QUIET=true 18 QUIET=true
19 VERBOSITY=ERROR 19 VERBOSITY=ERROR
20 @TMPDIR_OPTION@
20 21
21 && 22 &&
22 23
23 #else: 24 #else:
24 25
83 VALIDATION_STRINGENCY="${validation_stringency}" 84 VALIDATION_STRINGENCY="${validation_stringency}"
84 85
85 SORT_ORDER=coordinate 86 SORT_ORDER=coordinate
86 QUIET=true 87 QUIET=true
87 VERBOSITY=ERROR 88 VERBOSITY=ERROR
89 @TMPDIR_OPTION@
88 90
89 ]]></command> 91 ]]></command>
90 92
91 <inputs> 93 <inputs>
92 94