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comparison picard_DownsampleSam.xml @ 0:b76a4f17bbbb draft

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author devteam
date Thu, 23 Oct 2014 11:31:30 -0400
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1 <tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="1.122.0">
2 <description>Downsample a file to retain a subset of the reads</description>
3 <requirements>
4 <requirement type="package" version="1.122.0">picard</requirement>
5 </requirements>
6
7 <macros>
8 <import>picard_macros.xml</import>
9 </macros>
10
11 <command>
12 @java_options@
13 java -jar
14 \$JAVA_JAR_PATH/DownsampleSam.jar
15 INPUT="${inputFile}"
16 OUTPUT="${outFile}"
17 PROBABILITY=${probability}
18 RANDOM_SEED=${seed}
19 QUIET=true
20 VERBOSITY=ERROR
21 VALIDATION_STRINGENCY=${validation_stringency}
22 </command>
23 <inputs>
24 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset" />
25 <param name="probability" type="float" size="4" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
26 <param name="seed" type="integer" size="5" label="Random seed value" help="RANDOM_SEED; default=1" value="1" />
27
28 <expand macro="VS" />
29
30 </inputs>
31
32 <stdio>
33 <exit_code range="1:" level="fatal"/>
34 </stdio>
35
36 <outputs>
37 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/>
38 </outputs>
39
40 <tests>
41 <test>
42 <param name="inputFile" value="picard_DownsampleSam.bam" ftype="bam" />
43 <param name="probability" value="0.1" />
44 <param name="seed" value="1024" />
45 <param name="validation_stringency" value="LENIENT" />
46 <output name="outFile" file="picard_DownsampleSam_test1.bam" ftype="bam"/>
47 </test>
48 </tests>
49 <help>
50
51 .. class:: infomark
52
53 **Purpose**
54
55 Randomly down-sample a SAM or BAM file to retain a random subset of the reads. Mate-pairs are either both kept or both discarded. Reads marked as not primary alignments are all discarded. Each read is given a probability P of being retained - results with the exact same input in the same order and with the same value for RANDOM_SEED will produce the same results.
56
57 @dataset_collections@
58
59 @description@
60
61 INPUT=File
62 I=File The input SAM or BAM file to downsample. Required.
63
64 OUTPUT=File
65 O=File The output, downsampled, SAM or BAM file to write. Required.
66
67 RANDOM_SEED=Long
68 R=Long Random seed to use if reproducibilty is desired. Setting to null will cause multiple
69 invocations to produce different results.
70
71 PROBABILITY=Double
72 P=Double The probability of keeping any individual read, between 0 and 1.
73
74
75
76 @more_info@
77 </help>
78 </tool>