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comparison picard_AddOrReplaceReadGroups.xml @ 2:9227b8c3093b

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Updated command line format per dev team standards.
author devteam <devteam@galaxyproject.org>
date Tue, 02 Apr 2013 09:42:36 -0400
parents 1cd7f3b42609
children 3d4f1fa26f0e
comparison
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1:e0232cbac965 2:9227b8c3093b
1 <tool name="Add or Replace Groups" id="picard_ARRG" version="1.56.0"> 1 <tool name="Add or Replace Groups" id="picard_ARRG" version="1.56.0">
2 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> 2 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
3 <command interpreter="python"> 3 <command interpreter="python">
4 picard_wrapper.py 4 picard_wrapper.py
5 --input="$inputFile" 5 --input="${inputFile}"
6 --rg-lb="$rglb" 6 --rg-lb="${rglb}"
7 --rg-pl="$rgpl" 7 --rg-pl="${rgpl}"
8 --rg-pu="$rgpu" 8 --rg-pu="${rgpu}"
9 --rg-sm="$rgsm" 9 --rg-sm="${rgsm}"
10 --rg-id="$rgid" 10 --rg-id="${rgid}"
11 --rg-opts=${readGroupOpts.rgOpts} 11 --rg-opts="${readGroupOpts.rgOpts}"
12 #if $readGroupOpts.rgOpts == "full" 12 #if $readGroupOpts.rgOpts == "full"
13 --rg-cn="$readGroupOpts.rgcn" 13 --rg-cn="${readGroupOpts.rgcn}"
14 --rg-ds="$readGroupOpts.rgds" 14 --rg-ds="${readGroupOpts.rgds}"
15 #end if 15 #end if
16 --output-format=$outputFormat 16 --output-format="${outputFormat}"
17 --output=$outFile 17 --output="${outFile}"
18 -j "\$JAVA_JAR_PATH/AddOrReplaceReadGroups.jar" 18 -j "\$JAVA_JAR_PATH/AddOrReplaceReadGroups.jar"
19 --tmpdir "${__new_file_path__}" 19 --tmpdir "${__new_file_path__}"
20 </command> 20 </command>
21 <inputs> 21 <inputs>
22 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to add or replace read groups in" 22 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to add or replace read groups in"