annotate picard_macros.xml @ 8:3a3234d7a2e8 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 16 Jul 2015 15:53:10 -0400
parents 3d4f1fa26f0e
children 05087b27692a
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
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
10 <token name="@TOOL_VERSION@">1.136</token>
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>
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
14 <requirement type="package" version="1.136">picard</requirement>
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
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 <token name="@java_options@">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
20 _JAVA_OPTIONS=\${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} &amp;&amp;
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21 export _JAVA_OPTIONS &amp;&amp;
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22 </token>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 <token name="@more_info@">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
25 ------
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27 **Additional information**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
29 Additional information about Picard tools is available from Picard web site at http://broadinstitute.github.io/picard/.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 </token>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33 <token name="@description@">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 ------
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
35
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 **Inputs, outputs, and parameters**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
38 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
39
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 From Picard documentation( http://broadinstitute.github.io/picard/)::
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 </token>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 <token name="@RG@">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 -------
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 **Read Groups are Important!**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48 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
49
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 .. csv-table::
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 :header-rows: 1
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53 Tag,Importance,Definition,Meaning
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54 "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
55 "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
56 "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
57 "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
58
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59 **Example of Read Group usage**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
60
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61 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
62
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63 Dad's data:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64 @RG ID:FLOWCELL1.LANE1 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65 @RG ID:FLOWCELL1.LANE2 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66 @RG ID:FLOWCELL1.LANE3 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67 @RG ID:FLOWCELL1.LANE4 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69 Mom's data:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70 @RG ID:FLOWCELL1.LANE5 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
71 @RG ID:FLOWCELL1.LANE6 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72 @RG ID:FLOWCELL1.LANE7 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73 @RG ID:FLOWCELL1.LANE8 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75 Kid's data:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76 @RG ID:FLOWCELL2.LANE1 PL:illumina LB:LIB-KID-1 SM:KID PI:200
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
77 @RG ID:FLOWCELL2.LANE2 PL:illumina LB:LIB-KID-1 SM:KID PI:200
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
78 @RG ID:FLOWCELL2.LANE3 PL:illumina LB:LIB-KID-2 SM:KID PI:400
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
79 @RG ID:FLOWCELL2.LANE4 PL:illumina LB:LIB-KID-2 SM:KID PI:400
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
80
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
81 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
82 </token>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
83 <token name="@dataset_collections@">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
84 ------
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
85
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
86 **Dataset collections - processing large numbers of datasets at once**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
87
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
88 This will be added shortly
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
89
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
90
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
91 </token>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
92
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
93
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
94 </macros>