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comparison picard_DownsampleSam.xml @ 5:3d4f1fa26f0e draft

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author devteam
date Tue, 16 Dec 2014 19:03:21 -0500
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4:ab1f60c26526 5:3d4f1fa26f0e
1 <tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="1.126.0">
2 <description>Downsample a file to retain a subset of the reads</description>
3 <requirements>
4 <requirement type="package" version="1.126.0">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/picard.jar
15 DownsampleSam
16 INPUT="${inputFile}"
17 OUTPUT="${outFile}"
18 PROBABILITY=${probability}
19 RANDOM_SEED=${seed}
20 QUIET=true
21 VERBOSITY=ERROR
22 VALIDATION_STRINGENCY=${validation_stringency}
23 </command>
24 <inputs>
25 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset" />
26 <param name="probability" type="float" size="4" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
27 <param name="seed" type="integer" size="5" label="Random seed value" help="RANDOM_SEED; default=1" value="1" />
28
29 <expand macro="VS" />
30
31 </inputs>
32
33 <stdio>
34 <exit_code range="1:" level="fatal"/>
35 </stdio>
36
37 <outputs>
38 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/>
39 </outputs>
40
41 <tests>
42 <test>
43 <param name="inputFile" value="picard_DownsampleSam.bam" ftype="bam" />
44 <param name="probability" value="0.1" />
45 <param name="seed" value="1024" />
46 <param name="validation_stringency" value="LENIENT" />
47 <output name="outFile" file="picard_DownsampleSam_test1.bam" ftype="bam"/>
48 </test>
49 </tests>
50 <help>
51
52 .. class:: infomark
53
54 **Purpose**
55
56 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.
57
58 @dataset_collections@
59
60 @description@
61
62 INPUT=File
63 I=File The input SAM or BAM file to downsample. Required.
64
65 OUTPUT=File
66 O=File The output, downsampled, SAM or BAM file to write. Required.
67
68 RANDOM_SEED=Long
69 R=Long Random seed to use if reproducibilty is desired. Setting to null will cause multiple
70 invocations to produce different results.
71
72 PROBABILITY=Double
73 P=Double The probability of keeping any individual read, between 0 and 1.
74
75
76
77 @more_info@
78 </help>
79 </tool>