Mercurial > repos > devteam > picard

annotate picard_macros.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 6741a8ace658
children 2a17c789e0a5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
1 <macros>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <xml name="VS">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
3 <param name="validation_stringency" type="select" label="Select validation stringency" help=" Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
4 <option value="LENIENT" selected="True">Lenient</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
5 <option value="SILENT">Silent</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
6 <option value="STRICT">Strict</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
7 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
8 </xml>
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
9
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
10 <token name="@TOOL_VERSION@">2.18.2</token>
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
11
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
12 <xml name="requirements">
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
13 <requirements>
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
14 <requirement type="package" version="@TOOL_VERSION@">picard</requirement>
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
15 <yield/>
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
16 </requirements>
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
17 </xml>
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
18
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
19 <token name="@symlink_element_identifier@"><![CDATA[
14
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
20 #import re
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
21 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
22 ln -f -s '$inputFile' '$escaped_element_identifier' &&
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
23 ]]></token>
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
24
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
25 <token name="@java_options@"><![CDATA[
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
26 _JAVA_OPTIONS=\${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} &&
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
27 export _JAVA_OPTIONS &&
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
28 ]]></token>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
29
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
30 <token name="@handle_reference_source@"><![CDATA[
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
31 #if str( $reference_source.reference_source_selector ) == "history":
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
32 ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
33 #else:
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
34 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
35 #end if
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
36 ]]></token>
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
37
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
38 <token name="@more_info@">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 ------
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 **Additional information**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42
16
6741a8ace658 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 14
diff changeset
43 Additional information about Picard tools is available from Picard web site at http://broadinstitute.github.io/picard/ .
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 </token>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
45
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 <token name="@description@">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48 ------
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 **Inputs, outputs, and parameters**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52 Either a SAM file or a BAM file must be supplied. Galaxy automatically coordinate-sorts all uploaded BAM files.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54 From Picard documentation( http://broadinstitute.github.io/picard/)::
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56 </token>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57 <token name="@RG@">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
58 -------
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
60 **Read Groups are Important!**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
62 Setting read groups correctly from the start will simplify your life greatly because you can merge multiple BAM files into one significantly reducing the number of analysis steps. Below we provide an explanation of read groups fields taken from GATK FAQ webpage:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64 .. csv-table::
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65 :header-rows: 1
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
66
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67 Tag,Importance,Definition,Meaning
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68 "ID","Required","Read group identifier. Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section. Read group IDs may be modified when merging SAM files in order to handle collisions.","Ideally, this should be a globally unique identify across all sequencing data in the world, such as the Illumina flowcell + lane name and number. Will be referenced by each read with the RG:Z field, allowing tools to determine the read group information associated with each read, including the sample from which the read came. Also, a read group is effectively treated as a separate run of the NGS instrument in tools like base quality score recalibration (a GATK component) -- all reads within a read group are assumed to come from the same instrument run and to therefore share the same error model."
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69 "SM","Sample. Use pool name where a pool is being sequenced.","Required. As important as ID.","The name of the sample sequenced in this read group. GATK tools treat all read groups with the same SM value as containing sequencing data for the same sample. Therefore it's critical that the SM field be correctly specified, especially when using multi-sample tools like the Unified Genotyper (a GATK component)."
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70 "PL","Platform/technology used to produce the read. Valid values: ILLUMINA, SOLID, LS454, HELICOS and PACBIO.","Important. Not currently used in the GATK, but was in the past, and may return. The only way to known the sequencing technology used to generate the sequencing data","It's a good idea to use this field."
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
71 "LB","DNA preparation library identify","Essential for MarkDuplicates","MarkDuplicates uses the LB field to determine which read groups might contain molecular duplicates, in case the same DNA library was sequenced on multiple lanes."
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73 **Example of Read Group usage**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75 Support we have a trio of samples: MOM, DAD, and KID. Each has two DNA libraries prepared, one with 400 bp inserts and another with 200 bp inserts. Each of these libraries is run on two lanes of an illumina hiseq, requiring 3 x 2 x 2 = 12 lanes of data. When the data come off the sequencer, we would create 12 BAM files, with the following @RG fields in the header::
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
77 Dad's data:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
78 @RG ID:FLOWCELL1.LANE1 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
79 @RG ID:FLOWCELL1.LANE2 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
80 @RG ID:FLOWCELL1.LANE3 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
81 @RG ID:FLOWCELL1.LANE4 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
82
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
83 Mom's data:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
84 @RG ID:FLOWCELL1.LANE5 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
85 @RG ID:FLOWCELL1.LANE6 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
86 @RG ID:FLOWCELL1.LANE7 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
87 @RG ID:FLOWCELL1.LANE8 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
88
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
89 Kid's data:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
90 @RG ID:FLOWCELL2.LANE1 PL:illumina LB:LIB-KID-1 SM:KID PI:200
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
91 @RG ID:FLOWCELL2.LANE2 PL:illumina LB:LIB-KID-1 SM:KID PI:200
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
92 @RG ID:FLOWCELL2.LANE3 PL:illumina LB:LIB-KID-2 SM:KID PI:400
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
93 @RG ID:FLOWCELL2.LANE4 PL:illumina LB:LIB-KID-2 SM:KID PI:400
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
94
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
95 Note the hierarchical relationship between read groups (unique for each lane) to libraries (sequenced on two lanes) and samples (across four lanes, two lanes for each library).
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
96 </token>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
97 <token name="@dataset_collections@">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
98 ------
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
99
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
100 **Dataset collections - processing large numbers of datasets at once**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
101
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
102 This will be added shortly
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
103
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
104
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
105 </token>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
106
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
107 <xml name="citations">
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
108 <citations>
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
109 <citation type="bibtex">@misc{Picard,
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
110 author = {Broad Institute},
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
111 title = {Picard},
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
112 publisher = {GitHub},
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
113 journal = { Broad Institute, GitHub repository},
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
114 url = {http://broadinstitute.github.io/picard/}
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
115 }
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
116 </citation>
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
117 </citations>
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
118 </xml>
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 16
diff changeset
119
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
120
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
121 </macros>