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comparison picard_ReorderSam.xml @ 15:a5a13ea16d17 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 11:28:30 -0400
parents 486d7500da69
children 4740a2548206
comparison
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14:486d7500da69 15:a5a13ea16d17
1 <tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>reorder reads to match ordering in reference sequences</description> 2 <description>reorder reads to match ordering in reference sequences</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="${picard_dict}"
19 QUIET=true 19 QUIET=true
20 VERBOSITY=ERROR 20 VERBOSITY=ERROR
21 @TMPDIR_OPTION@
21 22
22 && 23 &&
23 24
24 #else: 25 #else:
25 26
36 ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}" 37 ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}"
37 38
38 VALIDATION_STRINGENCY="${validation_stringency}" 39 VALIDATION_STRINGENCY="${validation_stringency}"
39 QUIET=true 40 QUIET=true
40 VERBOSITY=ERROR 41 VERBOSITY=ERROR
42 @TMPDIR_OPTION@
41 43
42 ]]></command> 44 ]]></command>
43 45
44 <inputs> 46 <inputs>
45 47