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comparison picard_FixMateInformation.xml @ 12:05087b27692a 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 15:11:50 -0500
parents 3a3234d7a2e8
children 7e6fd3d0f16e
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11:efc56ee1ade4 12:05087b27692a
2 <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description> 2 <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command> 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 9
10 java -jar \$JAVA_JAR_PATH/picard.jar 10 picard
11 FixMateInformation 11 FixMateInformation
12 INPUT="${inputFile}" 12 INPUT="${inputFile}"
13 OUTPUT="${outFile}" 13 OUTPUT="${outFile}"
14 ASSUME_SORTED=${assume_sorted} 14 ASSUME_SORTED=${assume_sorted}
15 ADD_MATE_CIGAR=${add_mate_cigar} 15 ADD_MATE_CIGAR=${add_mate_cigar}
17 SORT_ORDER=coordinate 17 SORT_ORDER=coordinate
18 VALIDATION_STRINGENCY="${validation_stringency}" 18 VALIDATION_STRINGENCY="${validation_stringency}"
19 QUIET=true 19 QUIET=true
20 VERBOSITY=ERROR 20 VERBOSITY=ERROR
21 21
22 </command> 22 ]]></command>
23 <inputs> 23 <inputs>
24 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> 24 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
25 <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/> 25 <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
26 <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/> 26 <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/>
27 27
37 <test> 37 <test>
38 <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/> 38 <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/>
39 <param name="add_mate_cigar" value="True"/> 39 <param name="add_mate_cigar" value="True"/>
40 <param name="assume_sorted" value="False"/> 40 <param name="assume_sorted" value="False"/>
41 <param name="validation_stringency" value="LENIENT"/> 41 <param name="validation_stringency" value="LENIENT"/>
42 <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="2"/> 42 <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="4"/>
43 </test> 43 </test>
44 </tests> 44 </tests>
45 45
46 <stdio>
47 <exit_code range="1:" level="fatal"/>
48 </stdio>
49 46
50 <help> 47 <help>
51 48
52 **Purpose** 49 **Purpose**
53 50