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comparison picard_AddOrReplaceReadGroups.xml @ 7:08f69add4d06 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:36 -0500
parents 52fdfc45590a
children e417b1d6288d
comparison
equal deleted inserted replaced
6:961236c5ec73 7:08f69add4d06
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 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command> 8 <command detect_errors="exit_code">
9 @define_read_group_helpers@ 9 @define_read_group_helpers@
10 #set $rg_auto_name = $read_group_name_default($inputFile) 10 #set $rg_auto_name = $read_group_name_default($inputFile)
11 @set_read_group_vars@ 11 @set_read_group_vars@
12 @java_options@ 12 @java_options@
13 java -jar \$JAVA_JAR_PATH/picard.jar 13 picard
14 AddOrReplaceReadGroups 14 AddOrReplaceReadGroups
15 INPUT="${inputFile}" 15 INPUT="${inputFile}"
16 $format_read_group("RGLB=", $rg_lb, '"') 16 $format_read_group("RGLB=", $rg_lb, '"')
17 $format_read_group("RGPL=", $rg_pl, '"') 17 $format_read_group("RGPL=", $rg_pl, '"')
18 $format_read_group("RGPU=", $rg_pu, '"') 18 $format_read_group("RGPU=", $rg_pu, '"')
37 37
38 <outputs> 38 <outputs>
39 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/> 39 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
40 </outputs> 40 </outputs>
41 41
42 <stdio>
43 <exit_code range="1:" level="fatal"/>
44 </stdio>
45 42
46 <tests> 43 <tests>
47 <test> 44 <test>
48 <param name="inputFile" value="picard_ARRG.bam" /> 45 <param name="inputFile" value="picard_ARRG.bam" />
49 <param name="LB" value="tumor-a" /> 46 <param name="LB" value="tumor-a" />