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comparison picard_DownsampleSam.xml @ 8:e417b1d6288d draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:26 -0500
parents 08f69add4d06
children 41b8d087a2d2
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7:08f69add4d06 8:e417b1d6288d
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 detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 @symlink_element_identifier@
9 picard 10 picard
10 DownsampleSam 11 DownsampleSam
11 INPUT="${inputFile}" 12 INPUT='$inputFile.element_identifier'
12 OUTPUT="${outFile}" 13 OUTPUT="${outFile}"
13 PROBABILITY=${probability} 14 PROBABILITY=${probability}
14 RANDOM_SEED=${seed} 15 RANDOM_SEED=${seed}
15 QUIET=true 16 QUIET=true
16 VERBOSITY=ERROR 17 VERBOSITY=ERROR
18 ]]></command> 19 ]]></command>
19 <inputs> 20 <inputs>
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" /> 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" />
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" /> 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" />
22 <param name="seed" type="integer" label="Random seed value" help="RANDOM_SEED; default=1" value="1" /> 23 <param name="seed" type="integer" label="Random seed value" help="RANDOM_SEED; default=1" value="1" />
23 24
24 <expand macro="VS" /> 25 <expand macro="VS" />
25 26
26 </inputs> 27 </inputs>
27 28
28 29
29 <outputs> 30 <outputs>
30 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/> 31 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/>
31 </outputs> 32 </outputs>
32 33
33 <tests> 34 <tests>
34 <test> 35 <test>
35 <param name="inputFile" value="picard_DownsampleSam.bam" ftype="bam" /> 36 <param name="inputFile" value="picard_DownsampleSam.bam" ftype="bam" />
36 <param name="probability" value="0.1" /> 37 <param name="probability" value="0.1" />
37 <param name="seed" value="1024" /> 38 <param name="seed" value="1024" />
50 @dataset_collections@ 51 @dataset_collections@
51 52
52 @description@ 53 @description@
53 54
54 INPUT=File 55 INPUT=File
55 I=File The input SAM or BAM file to downsample. Required. 56 I=File The input SAM or BAM file to downsample. Required.
56 57
57 OUTPUT=File 58 OUTPUT=File
58 O=File The output, downsampled, SAM or BAM file to write. Required. 59 O=File The output, downsampled, SAM or BAM file to write. Required.
59 60
60 RANDOM_SEED=Long 61 RANDOM_SEED=Long
61 R=Long Random seed to use if reproducibilty is desired. Setting to null will cause multiple 62 R=Long Random seed to use if reproducibilty is desired. Setting to null will cause multiple
62 invocations to produce different results. 63 invocations to produce different results.
63 64
64 PROBABILITY=Double 65 PROBABILITY=Double
65 P=Double The probability of keeping any individual read, between 0 and 1. 66 P=Double The probability of keeping any individual read, between 0 and 1.
66 67
67 68
68 69
69 @more_info@ 70 @more_info@
70 </help> 71 </help>
71 </tool> 72 </tool>