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comparison picard_CleanSam.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
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6:961236c5ec73 7:08f69add4d06
2 <description>perform SAM/BAM grooming</description> 2 <description>perform SAM/BAM grooming</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 java -jar \$JAVA_JAR_PATH/picard.jar 9 picard
10 CleanSam 10 CleanSam
11 INPUT="${inputFile}" 11 INPUT="${inputFile}"
12 OUTPUT="${outFile}" 12 OUTPUT="${outFile}"
13 QUIET=true 13 QUIET=true
14 VERBOSITY=ERROR 14 VERBOSITY=ERROR
15 VALIDATION_STRINGENCY=${validation_stringency} 15 VALIDATION_STRINGENCY=${validation_stringency}
16 </command> 16 ]]></command>
17 17
18 <inputs> 18 <inputs>
19 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> 19 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
20 20
21 <expand macro="VS" /> 21 <expand macro="VS" />
25 <outputs> 25 <outputs>
26 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset"> 26 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset">
27 </data> 27 </data>
28 </outputs> 28 </outputs>
29 29
30 <stdio>
31 <exit_code range="1:" level="fatal"/>
32 </stdio>
33 30
34 <tests> 31 <tests>
35 <test> 32 <test>
36 <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" /> 33 <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" />
37 <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" /> 34 <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" />