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comparison picard_BedToIntervalList.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 f9242e01365a
comparison
equal deleted inserted replaced
19:5053a18d9bc8 20:2a17c789e0a5
1 <tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="BedToIntervalList" id="picard_BedToIntervalList" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>convert coordinate data into picard interval list format</description> 2 <description>convert coordinate data into picard interval list format</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 @symlink_element_identifier@ 10 @symlink_element_identifier@
16 #if str( $reference_source.reference_source_selector ) == "history": 16 #if str( $reference_source.reference_source_selector ) == "history":
17 17
18 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" 18 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
19 QUIET=true 19 QUIET=true
20 VERBOSITY=ERROR 20 VERBOSITY=ERROR
21 @TMPDIR_OPTION@
21 22
22 && 23 &&
23 24
24 #else: 25 #else:
25 26
34 OUTPUT="${outFile}" 35 OUTPUT="${outFile}"
35 36
36 SEQUENCE_DICTIONARY="${picard_dict}" 37 SEQUENCE_DICTIONARY="${picard_dict}"
37 QUIET=true 38 QUIET=true
38 VERBOSITY=ERROR 39 VERBOSITY=ERROR
40 @TMPDIR_OPTION@
39 41
40 ]]></command> 42 ]]></command>
41 43
42 <inputs> 44 <inputs>
43 45