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comparison picard_DownsampleSam.xml @ 0:5166ed57b1c4 draft

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Uploaded version 1.135
author avowinkel
date Mon, 06 Jul 2015 14:46:32 -0400
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1 <tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="1.135">
2 <description>Downsample a file to retain a subset of the reads</description>
3 <macros>
4 <import>picard_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>
8 @java_options@
9 java -jar
10 \$JAVA_JAR_PATH/picard.jar
11 DownsampleSam
12 INPUT="${inputFile}"
13 OUTPUT="${outFile}"
14 PROBABILITY=${probability}
15 RANDOM_SEED=${seed}
16 QUIET=true
17 VERBOSITY=ERROR
18 VALIDATION_STRINGENCY=${validation_stringency}
19 </command>
20 <inputs>
21 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset" />
22 <param name="probability" type="float" size="4" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
23 <param name="seed" type="integer" size="5" label="Random seed value" help="RANDOM_SEED; default=1" value="1" />
24
25 <expand macro="VS" />
26
27 </inputs>
28
29 <stdio>
30 <exit_code range="1:" level="fatal"/>
31 </stdio>
32
33 <outputs>
34 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/>
35 </outputs>
36
37 <tests>
38 <test>
39 <param name="inputFile" value="picard_DownsampleSam.bam" ftype="bam" />
40 <param name="probability" value="0.1" />
41 <param name="seed" value="1024" />
42 <param name="validation_stringency" value="LENIENT" />
43 <output name="outFile" file="picard_DownsampleSam_test1.bam" ftype="bam"/>
44 </test>
45 </tests>
46 <help>
47
48 .. class:: infomark
49
50 **Purpose**
51
52 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.
53
54 @dataset_collections@
55
56 @description@
57
58 INPUT=File
59 I=File The input SAM or BAM file to downsample. Required.
60
61 OUTPUT=File
62 O=File The output, downsampled, SAM or BAM file to write. Required.
63
64 RANDOM_SEED=Long
65 R=Long Random seed to use if reproducibilty is desired. Setting to null will cause multiple
66 invocations to produce different results.
67
68 PROBABILITY=Double
69 P=Double The probability of keeping any individual read, between 0 and 1.
70
71
72
73 @more_info@
74 </help>
75 </tool>