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comparison picard_DownsampleSam.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 5eaa8a968300
children 7e6fd3d0f16e
comparison
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11:efc56ee1ade4 12:05087b27692a
2 <description>Downsample a file to retain a subset of the reads</description> 2 <description>Downsample a file to retain a subset of the reads</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 9 picard
10 \$JAVA_JAR_PATH/picard.jar
11 DownsampleSam 10 DownsampleSam
12 INPUT="${inputFile}" 11 INPUT="${inputFile}"
13 OUTPUT="${outFile}" 12 OUTPUT="${outFile}"
14 PROBABILITY=${probability} 13 PROBABILITY=${probability}
15 RANDOM_SEED=${seed} 14 RANDOM_SEED=${seed}
16 QUIET=true 15 QUIET=true
17 VERBOSITY=ERROR 16 VERBOSITY=ERROR
18 VALIDATION_STRINGENCY=${validation_stringency} 17 VALIDATION_STRINGENCY=${validation_stringency}
19 </command> 18 ]]></command>
20 <inputs> 19 <inputs>
21 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset" /> 20 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset" />
22 <param name="probability" type="float" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" /> 21 <param name="probability" type="float" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
23 <param name="seed" type="integer" label="Random seed value" help="RANDOM_SEED; default=1" value="1" /> 22 <param name="seed" type="integer" label="Random seed value" help="RANDOM_SEED; default=1" value="1" />
24 23
25 <expand macro="VS" /> 24 <expand macro="VS" />
26 25
27 </inputs> 26 </inputs>
28 27
29 <stdio>
30 <exit_code range="1:" level="fatal"/>
31 </stdio>
32 28
33 <outputs> 29 <outputs>
34 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/> 30 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/>
35 </outputs> 31 </outputs>
36 32