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comparison picard_ReorderSam.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
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1:e0232cbac965 2:9227b8c3093b
1 <tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="1.56.0"> 1 <tool name="Reorder SAM/BAM" id="picard_ReorderSam" 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 #if $source.indexSource == "built-in" 6 #if $source.indexSource == "built-in"
7 --ref="${source.ref.fields.path}" 7 --ref="${source.ref.fields.path}"
8 #else 8 #else
9 --ref-file=$refFile 9 --ref-file="${refFile}"
10 --species-name=$source.speciesName 10 --species-name="${source.speciesName}"
11 --build-name=$source.buildName 11 --build-name="${source.buildName}"
12 --trunc-names=$source.truncateSeqNames 12 --trunc-names="${source.truncateSeqNames}"
13 #end if 13 #end if
14 --allow-inc-dict-concord=$allowIncDictConcord 14 --allow-inc-dict-concord="${allowIncDictConcord}"
15 --allow-contig-len-discord=$allowContigLenDiscord 15 --allow-contig-len-discord="${allowContigLenDiscord}"
16 --output-format=$outputFormat 16 --output-format="${outputFormat}"
17 --output=$outFile 17 --output="${outFile}"
18 --tmpdir "${__new_file_path__}" 18 --tmpdir "${__new_file_path__}"
19 -j "\$JAVA_JAR_PATH/ReorderSam.jar" 19 -j "\$JAVA_JAR_PATH/ReorderSam.jar"
20 </command> 20 </command>
21 <inputs> 21 <inputs>
22 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered" 22 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered"