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comparison bwa_macros.xml @ 4:ac30bfd3e2a8 draft

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planemo upload commit a50a3947aebc8a1d11bac39599f4efd8ed9a3bd5
author devteam
date Thu, 18 Jun 2015 17:35:40 -0400
parents e29bc5c169bc
children fbf460831036
comparison
equal deleted inserted replaced
3:607ca4b95837 4:ac30bfd3e2a8
1 <macros> 1 <macros>
2 2
3 <token name="@set_rg_string@"> 3 <token name="@set_rg_string@">
4 #set $rg_string = "@RG\tID:" + str($rg.ID) + "\tSM:" + str($rg.SM) + "\tPL:" + str($rg.PL) 4 #set $rg_string = "@RG\tID:" + str($rg.ID) + "\tSM:" + str($rg.SM) + "\tPL:" + str($rg.PL)
5 #if $rg.LB 5 #if $rg.LB
6 #set $rg_string += "\tLB:$rg.LB" 6 #set $rg_string += "\tLB:" + str($rg.LB)
7 #end if 7 #end if
8 #if $rg.CN 8 #if $rg.CN
9 #set $rg_string += "\tCN:$rg.CN" 9 #set $rg_string += "\tCN:" + str($rg.CN)
10 #end if 10 #end if
11 #if $rg.DS 11 #if $rg.DS
12 #set $rg_string += "\tDS:$rg.DS" 12 #set $rg_string += "\tDS:" + str($rg.DS)
13 #end if 13 #end if
14 #if $rg.DT 14 #if $rg.DT
15 #set $rg_string += "\tDT:$rg.DT" 15 #set $rg_string += "\tDT:" + str($rg.DT)
16 #end if 16 #end if
17 #if $rg.FO 17 #if $rg.FO
18 #set $rg_string += "\tFO:$rg.FO" 18 #set $rg_string += "\tFO:" + str($rg.FO)
19 #end if 19 #end if
20 #if $rg.KS 20 #if $rg.KS
21 #set $rg_string += "\tKS:$rg.KS" 21 #set $rg_string += "\tKS:" + str($rg.KS)
22 #end if 22 #end if
23 #if $rg.PG 23 #if $rg.PG
24 #set $rg_string += "\tPG:$rg.PG" 24 #set $rg_string += "\tPG:" + str($rg.PG)
25 #end if 25 #end if
26 #if str($rg.PI) 26 #if str($rg.PI)
27 #set $rg_string += "\tPI:$rg.PI" 27 #set $rg_string += "\tPI:" + str($rg.PI)
28 #end if 28 #end if
29 #if $rg.PU 29 #if $rg.PU
30 #set $rg_string += "\tPU:$rg.PU" 30 #set $rg_string += "\tPU:" + str($rg.PU)
31 #end if 31 #end if
32 </token> 32 </token>
33 33
34 <token name="@RG@"> 34 <token name="@RG@">
35 ----- 35 -----
36 36
37 .. class:: warningmark 37 .. class:: warningmark
38 38
39 **Read Groups are Important!** 39 **Read Groups are Important!**
40 40
41 One of the recommended best practices in NGS analysis is adding read group information to BAM files. You can do thid directly in BWA interface using the 41 One of the recommended best practices in NGS analysis is adding read group information to BAM files. You can do this directly in BWA interface using the
42 **Specify read group information?** widget. If you are not familiar with read groups you shold know that this is effectively a way to tag reads with an additional ID. 42 **Specify read group information?** widget. If you are not familiar with read groups you shold know that this is effectively a way to tag reads with an additional ID.
43 This allows you to combine BAM files from, for example, multiple BWA runs into a single dataset. This significantly simplifies downstream processing as 43 This allows you to combine BAM files from, for example, multiple BWA runs into a single dataset. This significantly simplifies downstream processing as
44 instead of dealing with multiple datasets you only have to handle only one. This is possible because the read group information allows you to identify 44 instead of dealing with multiple datasets you only have to handle only one. This is possible because the read group information allows you to identify
45 data from different experiments even if they are combined in one file. Many downstream analysis tools such as varinat callers (e.g., FreeBayes or Naive Varinat Caller 45 data from different experiments even if they are combined in one file. Many downstream analysis tools such as varinat callers (e.g., FreeBayes or Naive Varinat Caller
46 present in Galaxy) are aware of readgtroups and will automatically generate calls for each individual sample even if they are combined within a single file. 46 present in Galaxy) are aware of readgtroups and will automatically generate calls for each individual sample even if they are combined within a single file.
102 <token name="@dataset_collections@"> 102 <token name="@dataset_collections@">
103 ------ 103 ------
104 104
105 **Dataset collections - processing large numbers of datasets at once** 105 **Dataset collections - processing large numbers of datasets at once**
106 106
107 This will be added shortly 107 Dataset collections are in beta-testing. Extensive documentation will be added later this Spring.
108 108
109 109
110 </token> 110 </token>
111 <xml name="readgroup_params"> 111 <xml name="readgroup_params">
112 <conditional name="rg"> 112 <conditional name="rg">
113 <param name="rg_selector" type="select" label="Set read groups information?" help="-R; Specifying read group information can greatly simplify your downstream analyses by allowing combining multiple datasets. See help below for more details"> 113 <param name="rg_selector" type="select" label="Set read groups information?" help="(-R in bwa mem; -r in bwa aln); Specifying read group information can greatly simplify your downstream analyses by allowing combining multiple datasets. See help below for more details">
114 <option value="set">Set</option> 114 <option value="set">Set</option>
115 <option value="do_not_set" selected="True">Do not set</option> 115 <option value="do_not_set" selected="True">Do not set</option>
116 </param> 116 </param>
117 <when value="set"> 117 <when value="set">
118 <param name="ID" type="text" value="" size="20" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment"> 118 <param name="ID" type="text" value="" size="20" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment">
120 </param> 120 </param>
121 <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" /> 121 <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" />
122 <param name="PL" type="select" label="Platform/technology used to produce the reads (PL)"> 122 <param name="PL" type="select" label="Platform/technology used to produce the reads (PL)">
123 <option value="CAPILLARY">CAPILLARY</option> 123 <option value="CAPILLARY">CAPILLARY</option>
124 <option value="LS454">LS454</option> 124 <option value="LS454">LS454</option>
125 <option value="ILLUMINA">ILLUMINA</option> 125 <option selected="True" value="ILLUMINA">ILLUMINA</option>
126 <option value="SOLID">SOLID</option> 126 <option value="SOLID">SOLID</option>
127 <option value="HELICOS">HELICOS</option> 127 <option value="HELICOS">HELICOS</option>
128 <option value="IONTORRENT">IONTORRENT</option> 128 <option value="IONTORRENT">IONTORRENT</option>
129 <option value="PACBIO">PACBIO</option> 129 <option value="PACBIO">PACBIO</option>
130 </param> 130 </param>