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comparison picard_macros.xml @ 12:05087b27692a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:50 -0500
parents 3a3234d7a2e8
children 7e6fd3d0f16e
comparison
equal deleted inserted replaced
11:efc56ee1ade4 12:05087b27692a
5 <option value="SILENT">Silent</option> 5 <option value="SILENT">Silent</option>
6 <option value="STRICT">Strict</option> 6 <option value="STRICT">Strict</option>
7 </param> 7 </param>
8 </xml> 8 </xml>
9 9
10 <token name="@TOOL_VERSION@">1.136</token> 10 <token name="@TOOL_VERSION@">2.7.1</token>
11 11
12 <xml name="requirements"> 12 <xml name="requirements">
13 <requirements> 13 <requirements>
14 <requirement type="package" version="1.136">picard</requirement> 14 <requirement type="package" version="2.7.1">picard</requirement>
15 <yield/> 15 <yield/>
16 </requirements> 16 </requirements>
17 </xml> 17 </xml>
18 18
19 <token name="@java_options@"> 19 <token name="@java_options@"><![CDATA[
20 _JAVA_OPTIONS=\${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} &amp;&amp; 20 _JAVA_OPTIONS=\${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} &&
21 export _JAVA_OPTIONS &amp;&amp; 21 export _JAVA_OPTIONS &&
22 </token> 22 ]]></token>
23 23
24 <token name="@more_info@"> 24 <token name="@more_info@">
25 ------ 25 ------
26 26
27 **Additional information** 27 **Additional information**
28 28
29 Additional information about Picard tools is available from Picard web site at http://broadinstitute.github.io/picard/. 29 Additional information about Picard tools is available from Picard web site at http://broadinstitute.github.io/picard/.
30 </token> 30 </token>
31 31
32 32
33 <token name="@description@"> 33 <token name="@description@">
34 ------ 34 ------
35 35
36 **Inputs, outputs, and parameters** 36 **Inputs, outputs, and parameters**
47 47
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: 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:
49 49
50 .. csv-table:: 50 .. csv-table::
51 :header-rows: 1 51 :header-rows: 1
52 52
53 Tag,Importance,Definition,Meaning 53 Tag,Importance,Definition,Meaning
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." 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."
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)." 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)."
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." 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."
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." 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."
63 Dad's data: 63 Dad's data:
64 @RG ID:FLOWCELL1.LANE1 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200 64 @RG ID:FLOWCELL1.LANE1 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200
65 @RG ID:FLOWCELL1.LANE2 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200 65 @RG ID:FLOWCELL1.LANE2 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200
66 @RG ID:FLOWCELL1.LANE3 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400 66 @RG ID:FLOWCELL1.LANE3 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400
67 @RG ID:FLOWCELL1.LANE4 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400 67 @RG ID:FLOWCELL1.LANE4 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400
68 68
69 Mom's data: 69 Mom's data:
70 @RG ID:FLOWCELL1.LANE5 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200 70 @RG ID:FLOWCELL1.LANE5 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200
71 @RG ID:FLOWCELL1.LANE6 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200 71 @RG ID:FLOWCELL1.LANE6 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200
72 @RG ID:FLOWCELL1.LANE7 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400 72 @RG ID:FLOWCELL1.LANE7 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400
73 @RG ID:FLOWCELL1.LANE8 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400 73 @RG ID:FLOWCELL1.LANE8 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400
74 74
75 Kid's data: 75 Kid's data:
76 @RG ID:FLOWCELL2.LANE1 PL:illumina LB:LIB-KID-1 SM:KID PI:200 76 @RG ID:FLOWCELL2.LANE1 PL:illumina LB:LIB-KID-1 SM:KID PI:200
77 @RG ID:FLOWCELL2.LANE2 PL:illumina LB:LIB-KID-1 SM:KID PI:200 77 @RG ID:FLOWCELL2.LANE2 PL:illumina LB:LIB-KID-1 SM:KID PI:200
78 @RG ID:FLOWCELL2.LANE3 PL:illumina LB:LIB-KID-2 SM:KID PI:400 78 @RG ID:FLOWCELL2.LANE3 PL:illumina LB:LIB-KID-2 SM:KID PI:400
79 @RG ID:FLOWCELL2.LANE4 PL:illumina LB:LIB-KID-2 SM:KID PI:400 79 @RG ID:FLOWCELL2.LANE4 PL:illumina LB:LIB-KID-2 SM:KID PI:400
87 87
88 This will be added shortly 88 This will be added shortly
89 89
90 90
91 </token> 91 </token>
92 92
93 93
94 </macros> 94 </macros>