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comparison picard_FilterSamReads.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="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>include or exclude aligned and unaligned reads and read lists</description> 2 <description>include or exclude aligned and unaligned reads and read lists</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 OUTPUT=query_sorted_bam.bam 16 OUTPUT=query_sorted_bam.bam
17 SORT_ORDER=queryname 17 SORT_ORDER=queryname
18 VALIDATION_STRINGENCY=LENIENT 18 VALIDATION_STRINGENCY=LENIENT
19 QUIET=true 19 QUIET=true
20 VERBOSITY=ERROR 20 VERBOSITY=ERROR
21 @TMPDIR_OPTION@
21 22
22 && 23 &&
23 24
24 picard 25 picard
25 FilterSamReads 26 FilterSamReads
33 OUTPUT="${outFile}" 34 OUTPUT="${outFile}"
34 SORT_ORDER=coordinate 35 SORT_ORDER=coordinate
35 VALIDATION_STRINGENCY="${validation_stringency}" 36 VALIDATION_STRINGENCY="${validation_stringency}"
36 QUIET=true 37 QUIET=true
37 VERBOSITY=ERROR 38 VERBOSITY=ERROR
39 @TMPDIR_OPTION@
38 40
39 ]]></command> 41 ]]></command>
40 <inputs> 42 <inputs>
41 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> 43 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
42 <conditional name="filter_type"> 44 <conditional name="filter_type">