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comparison picard_CollectAlignmentSummaryMetrics.xml @ 19:5053a18d9bc8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
author iuc
date Mon, 16 Apr 2018 21:27:29 -0400
parents 465cbb0cf2eb
children 2a17c789e0a5
comparison
equal deleted inserted replaced
18:7615ac66c6e5 19:5053a18d9bc8
1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.1"> 1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>writes a file containing summary alignment metrics</description> 2 <description>writes a file containing summary alignment metrics</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 </macros> 6 </macros>
6 <expand macro="requirements" /> 7 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 9 @java_options@
9 @symlink_element_identifier@ 10 @symlink_element_identifier@
10 ##set up input files 11 ##set up input files
11 12
12 #set $reference_fasta_filename = "localref.fa" 13 #set $reference_fasta_filename = "localref.fa"
13 14
14 #if str( $reference_source.reference_source_selector ) == "history": 15 @handle_reference_source@
15 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
16 #else:
17 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
18 #end if
19 16
20 picard 17 picard
21 CollectAlignmentSummaryMetrics 18 CollectAlignmentSummaryMetrics
22 INPUT='$escaped_element_identifier' 19 INPUT='$escaped_element_identifier'
23 OUTPUT="${outFile}" 20 OUTPUT="${outFile}"
120 AS=Boolean If true (default), then the sort order in the header file will be ignored. 117 AS=Boolean If true (default), then the sort order in the header file will be ignored.
121 118
122 @more_info@ 119 @more_info@
123 120
124 </help> 121 </help>
122 <expand macro="citations" />
125 </tool> 123 </tool>
126
127