Mercurial > repos > devteam > picard

annotate picard_DownsampleSam.xml @ 19:5053a18d9bc8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
author iuc
date Mon, 16 Apr 2018 21:27:29 -0400
parents 465cbb0cf2eb
children 2a17c789e0a5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
1 <tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>Downsample a file to retain a subset of the reads</description>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
3 <macros>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
4 <import>picard_macros.xml</import>
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
5 <token name="@WRAPPER_VERSION@">0</token>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
6 </macros>
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
7 <expand macro="requirements" />
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
9 @java_options@
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
10 @symlink_element_identifier@
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
11 picard
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
12 DownsampleSam
14
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
13 INPUT='$escaped_element_identifier'
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
14 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
15 PROBABILITY=${probability}
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
16 RANDOM_SEED=${seed}
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
17 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
18 VERBOSITY=ERROR
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 VALIDATION_STRINGENCY=${validation_stringency}
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
20 ]]></command>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22 <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" />
9
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
23 <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" />
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
24 <param name="seed" type="integer" label="Random seed value" help="RANDOM_SEED; default=1" value="1" />
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
25
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 <expand macro="VS" />
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
27
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 </inputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
29
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
30
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33 </outputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
34
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
35 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37 <param name="inputFile" value="picard_DownsampleSam.bam" ftype="bam" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
38 <param name="probability" value="0.1" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 <param name="seed" value="1024" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 <param name="validation_stringency" value="LENIENT" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 <output name="outFile" file="picard_DownsampleSam_test1.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 </tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 .. class:: infomark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 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.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56 INPUT=File
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
57 I=File The input SAM or BAM file to downsample. Required.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
58
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59 OUTPUT=File
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
60 O=File The output, downsampled, SAM or BAM file to write. Required.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
62 RANDOM_SEED=Long
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63 R=Long Random seed to use if reproducibilty is desired. Setting to null will cause multiple
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64 invocations to produce different results.
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
65
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66 PROBABILITY=Double
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
67 P=Double The probability of keeping any individual read, between 0 and 1.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
68
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
71 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72 </help>
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
73 <expand macro="citations" />
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74 </tool>