Mercurial > repos > devteam > picard

annotate picard_DownsampleSam.xml @ 33:3f254c5ced1d draft default tip

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 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
33
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
1 <tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
2 <description>Downsample a file to retain a subset of the reads</description>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
3 <macros>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
4 <import>picard_macros.xml</import>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
5 <token name="@WRAPPER_VERSION@">0</token>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
6 </macros>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
7 <expand macro="requirements"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
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
33
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
13 --INPUT '$escaped_element_identifier'
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
14 --OUTPUT '${outFile}'
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
15 --PROBABILITY ${probability}
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
16 --RANDOM_SEED ${seed}
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
17 --QUIET true
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
18 --VERBOSITY ERROR
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
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>
33
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
21 <inputs>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
22 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
23 <param name="probability" type="float" min="0.0" max="1.0" value="1" 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"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
24 <param name="seed" type="integer" value="1" label="Random seed value" help="RANDOM_SEED; default=1"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
25 <expand macro="VS"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
26 </inputs>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
27 <outputs>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
28 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
29 </outputs>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
30 <tests>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
31 <test>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
32 <param name="inputFile" value="picard_DownsampleSam.bam" ftype="bam"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
33 <param name="probability" value="0.1"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
34 <param name="seed" value="1024"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
35 <param name="validation_stringency" value="LENIENT"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
36 <output name="outFile" file="picard_DownsampleSam_test1.bam" ftype="bam" lines_diff="2"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
37 </test>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
38 </tests>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
39 <help>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 .. class:: infomark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45 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
46
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 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
52 I=File The input SAM or BAM file to downsample. Required.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54 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
55 O=File The output, downsampled, SAM or BAM file to write. Required.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57 RANDOM_SEED=Long
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
58 R=Long Random seed to use if reproducibilty is desired. Setting to null will cause multiple
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59 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
60
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61 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
62 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
63
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67 </help>
33
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
diff changeset
68 <expand macro="citations"/>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69 </tool>