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comparison picard_AddOrReplaceReadGroups.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 c943f4a04af0
comparison
equal deleted inserted replaced
14:486d7500da69 15:a5a13ea16d17
1 <tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>add or replaces read group information</description> 2 <description>add or replaces read group information</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 <import>read_group_macros.xml</import> 5 <import>read_group_macros.xml</import>
6 <token name="@WRAPPER_VERSION@">0</token> 6 <token name="@WRAPPER_VERSION@">1</token>
7 </macros> 7 </macros>
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
9 <command detect_errors="exit_code"> 9 <command detect_errors="exit_code"><![CDATA[
10 @define_read_group_helpers@ 10 @define_read_group_helpers@
11 #set $rg_auto_name = $read_group_name_default($inputFile) 11 #set $rg_auto_name = $read_group_name_default($inputFile)
12 @set_read_group_vars@ 12 @set_read_group_vars@
13 @java_options@ 13 @java_options@
14 @symlink_element_identifier@ 14 @symlink_element_identifier@
24 $format_read_group("RGPI=", $rg_pi, '"') 24 $format_read_group("RGPI=", $rg_pi, '"')
25 $format_read_group("RGDT=", $rg_dt, '"') 25 $format_read_group("RGDT=", $rg_dt, '"')
26 VALIDATION_STRINGENCY="${validation_stringency}" 26 VALIDATION_STRINGENCY="${validation_stringency}"
27 QUIET=true 27 QUIET=true
28 VERBOSITY=ERROR 28 VERBOSITY=ERROR
29 @TMPDIR_OPTION@
29 OUTPUT="${outFile}" 30 OUTPUT="${outFile}"
30 31
31 </command> 32 ]]></command>
32 33
33 <inputs> 34 <inputs>
34 <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> 35 <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
35 <expand macro="read_group_inputs_picard" /> 36 <expand macro="read_group_inputs_picard" />
36 <expand macro="VS" /> 37 <expand macro="VS" />