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comparison picard_MarkDuplicatesWithMateCigar.xml @ 8:3a3234d7a2e8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 16 Jul 2015 15:53:10 -0400
parents 4ff1e04010e6
children 5eaa8a968300
comparison
equal deleted inserted replaced
7:379fdf4c41ac 8:3a3234d7a2e8
1 <tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="1.126.0"> 1 <tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="@TOOL_VERSION@.0">
2 <description>examine aligned records in BAM datasets to locate duplicate molecules</description> 2 <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
3 <requirements>
4 <requirement type="package" version="1.126.0">picard</requirement>
5 </requirements>
6
7 <macros> 3 <macros>
8 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
9 </macros> 5 </macros>
10 6 <expand macro="requirements" />
11 <command> 7 <command>
12 @java_options@ 8 @java_options@
13 9
14 java -jar \$JAVA_JAR_PATH/picard.jar 10 java -jar \$JAVA_JAR_PATH/picard.jar
15 MarkDuplicatesWithMateCigar 11 MarkDuplicatesWithMateCigar
16 12
17 INPUT="${inputFile}" 13 INPUT="${inputFile}"
18 OUTPUT="${outFile}" 14 OUTPUT="${outFile}"
19 15
20 METRICS_FILE="${metrics_file}" 16 METRICS_FILE="${metrics_file}"
21 #for $element in $comments: 17 COMMENT="${comment}"
22 COMMENT="${element.comment}" 18
23 #end for
24
25 MINIMUM_DISTANCE="${minimum_distance}" 19 MINIMUM_DISTANCE="${minimum_distance}"
26 SKIP_PAIRS_WITH_NO_MATE_CIGAR="${skip_pairs_with_no_mate_cigar}" 20 SKIP_PAIRS_WITH_NO_MATE_CIGAR="${skip_pairs_with_no_mate_cigar}"
27 21
28 22
29 REMOVE_DUPLICATES="${remove_duplicates}" 23 REMOVE_DUPLICATES="${remove_duplicates}"