Mercurial > repos > devteam > bwa

annotate bwa_macros.xml @ 19:dfd8b7f78c37 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/bwa commit a161a3a7e9149a5ba63fe20f435cd2f275dce4c8
author iuc
date Fri, 22 Dec 2017 15:03:03 -0500
parents 48f306c57611
children 4f774c1e6049
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
1 <macros>
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
2 <import>read_group_macros.xml</import>
11
546ada4a9f43 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 610045611b00099e0a24183c8cf33aebfa9635cf
devteam
parents: 9
diff changeset
3
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
4 <token name="@VERSION@">0.7.17</token>
11
546ada4a9f43 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 610045611b00099e0a24183c8cf33aebfa9635cf
devteam
parents: 9
diff changeset
5
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
6 <token name="@set_rg_string@">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
7 #set $rg_string = "@RG\\tID:" + str($rg_id)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
8 #set $rg_string += $format_read_group("\\tSM:", $rg_sm)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
9 #set $rg_string += $format_read_group("\\tPL:", $rg_pl)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
10 #set $rg_string += $format_read_group("\\tLB:", $rg_lb)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
11 #set $rg_string += $format_read_group("\\tCN:", $rg_cn)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
12 #set $rg_string += $format_read_group("\\tDS:", $rg_ds)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
13 #set $rg_string += $format_read_group("\\tDT:", $rg_dt)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
14 #set $rg_string += $format_read_group("\\tFO:", $rg_fo)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
15 #set $rg_string += $format_read_group("\\tKS:", $rg_ks)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
16 #set $rg_string += $format_read_group("\\tPG:", $rg_pg)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
17 #set $rg_string += $format_read_group("\\tPI:", $rg_pi)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
18 #set $rg_string += $format_read_group("\\tPU:", $rg_pu)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
19 </token>
6
09a7281d24c5 planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
20
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
21 <token name="@set_reference_fasta_filename@"><![CDATA[
11
546ada4a9f43 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 610045611b00099e0a24183c8cf33aebfa9635cf
devteam
parents: 9
diff changeset
22 #if str( $reference_source.reference_source_selector ) == "history":
546ada4a9f43 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 610045611b00099e0a24183c8cf33aebfa9635cf
devteam
parents: 9
diff changeset
23 #set $reference_fasta_filename = "localref.fa"
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
24 ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
11
546ada4a9f43 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 610045611b00099e0a24183c8cf33aebfa9635cf
devteam
parents: 9
diff changeset
25 bwa index
546ada4a9f43 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 610045611b00099e0a24183c8cf33aebfa9635cf
devteam
parents: 9
diff changeset
26 #if str($reference_source.index_a) != 'auto'
546ada4a9f43 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 610045611b00099e0a24183c8cf33aebfa9635cf
devteam
parents: 9
diff changeset
27 -a ${reference_source.index_a}
546ada4a9f43 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 610045611b00099e0a24183c8cf33aebfa9635cf
devteam
parents: 9
diff changeset
28 #end if
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
29 '${reference_fasta_filename}' &&
11
546ada4a9f43 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 610045611b00099e0a24183c8cf33aebfa9635cf
devteam
parents: 9
diff changeset
30 #else:
546ada4a9f43 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 610045611b00099e0a24183c8cf33aebfa9635cf
devteam
parents: 9
diff changeset
31 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
546ada4a9f43 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 610045611b00099e0a24183c8cf33aebfa9635cf
devteam
parents: 9
diff changeset
32 #end if
546ada4a9f43 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 610045611b00099e0a24183c8cf33aebfa9635cf
devteam
parents: 9
diff changeset
33 ]]></token>
546ada4a9f43 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 610045611b00099e0a24183c8cf33aebfa9635cf
devteam
parents: 9
diff changeset
34
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
35 <xml name="requirements">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
36 <requirements>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
37 <requirement type="package" version="@VERSION@">bwa</requirement>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
38 <requirement type="package" version="1.6">samtools</requirement>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
39 </requirements>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
40 </xml>
7
d8c9597bfb09 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd
devteam
parents: 6
diff changeset
41
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
42 <xml name="stdio">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
43 <stdio>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
44 <exit_code range="1:" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
45 <exit_code range=":-1" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
46 <regex match="Error:" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
47 <regex match="Exception:" />
19
dfd8b7f78c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit a161a3a7e9149a5ba63fe20f435cd2f275dce4c8
iuc
parents: 18
diff changeset
48 <regex match="\[bns_restore_core\] Parse error reading" />
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
49 </stdio>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
50 </xml>
6
09a7281d24c5 planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
51
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
52 <macro name="reference_source_conditional">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
53 <conditional name="reference_source">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
54 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
55 <option value="cached">Use a built-in genome index</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
56 <option value="history">Use a genome from history and build index</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
57 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
58 <when value="cached">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
59 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
60 <options from_data_table="bwa_mem_indexes">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
61 <filter type="sort_by" column="2" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
62 <validator type="no_options" message="No indexes are available" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
63 </options>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
64 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
65 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
66 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
67 <when value="history">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
68 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
69 <param name="index_a" type="select" label="Algorithm for constructing the BWT index" help="(-a)">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
70 <option value="auto">Auto. Let BWA decide the best algorithm to use</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
71 <option value="is">IS linear-time algorithm for constructing suffix array. It requires 5.37N memory where N is the size of the database. IS is moderately fast, but does not work with database larger than 2GB</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
72 <option value="bwtsw">BWT-SW algorithm. This method works also with big genomes</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
73 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
74 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
75 </conditional>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
76 </macro>
11
546ada4a9f43 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 610045611b00099e0a24183c8cf33aebfa9635cf
devteam
parents: 9
diff changeset
77
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
78 <macro name="dbKeyActionsBwa">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
79 <expand macro="dbKeyActions">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
80 <option type="from_data_table" name="bwa_indexes" column="1" offset="0">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
81 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
82 <filter type="param_value" ref="reference_source.ref_file" column="0"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
83 </option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
84 </expand>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
85 </macro>
6
09a7281d24c5 planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
86
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
87 <macro name="dbKeyActionsBwaMem">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
88 <expand macro="dbKeyActions">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
89 <option type="from_data_table" name="bwa_mem_indexes" column="1" offset="0">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
90 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
91 <filter type="param_value" ref="reference_source.ref_file" column="0"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
92 </option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
93 </expand>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
94 </macro>
6
09a7281d24c5 planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
95
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
96 <macro name="dbKeyActions">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
97 <actions>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
98 <conditional name="reference_source.reference_source_selector">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
99 <when value="cached">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
100 <action type="metadata" name="dbkey">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
101 <yield />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
102 </action>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
103 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
104 <when value="history">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
105 <action type="metadata" name="dbkey">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
106 <option type="from_param" name="reference_source.ref_file" param_attribute="dbkey" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
107 </action>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
108 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
109 </conditional>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
110 </actions>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
111 </macro>
6
09a7281d24c5 planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
112
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
113 <token name="@RG@">
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
114 -----
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
115
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
116 .. class:: warningmark
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
117
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
118 **Read Groups are Important!**
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
119
4
ac30bfd3e2a8 planemo upload commit a50a3947aebc8a1d11bac39599f4efd8ed9a3bd5
devteam
parents: 2
diff changeset
120 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
2
e29bc5c169bc Uploaded
devteam
parents: 0
diff changeset
121 **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.
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
122 This allows you to combine BAM files from, for example, multiple BWA runs into a single dataset. This significantly simplifies downstream processing as
2
e29bc5c169bc Uploaded
devteam
parents: 0
diff changeset
123 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
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
124 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
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
125 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.
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
126
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
127 **Description of read groups fields**
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
128
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
129 (from GATK FAQ webpage):
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
130
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
131 .. csv-table::
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
132 :header-rows: 1
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
133
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
134 Tag,Importance,Definition,Meaning
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
135 "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."
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
136 "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)."
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
137 "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."
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
138 "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."
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
139
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
140
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
141 **Example of Read Group usage**
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
142
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
143 Suppose 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::
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
144
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
145 Dad's data:
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
146 @RG ID:FLOWCELL1.LANE1 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
147 @RG ID:FLOWCELL1.LANE2 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
148 @RG ID:FLOWCELL1.LANE3 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
149 @RG ID:FLOWCELL1.LANE4 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
150
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
151 Mom's data:
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
152 @RG ID:FLOWCELL1.LANE5 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
153 @RG ID:FLOWCELL1.LANE6 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
154 @RG ID:FLOWCELL1.LANE7 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
155 @RG ID:FLOWCELL1.LANE8 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
156
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
157 Kid's data:
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
158 @RG ID:FLOWCELL2.LANE1 PL:illumina LB:LIB-KID-1 SM:KID PI:200
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
159 @RG ID:FLOWCELL2.LANE2 PL:illumina LB:LIB-KID-1 SM:KID PI:200
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
160 @RG ID:FLOWCELL2.LANE3 PL:illumina LB:LIB-KID-2 SM:KID PI:400
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
161 @RG ID:FLOWCELL2.LANE4 PL:illumina LB:LIB-KID-2 SM:KID PI:400
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
162
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
163 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).
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
164 </token>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
165 <token name="@info@">
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
166 -----
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
167
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
168 .. class:: infomark
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
169
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
170 **More info**
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
171
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
172 To obtain more information about BWA and ask questions use these resources:
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
173
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
174 1. https://biostar.usegalaxy.org/
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
175 2. https://www.biostars.org/
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
176 3. https://github.com/lh3/bwa
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
177 4. http://bio-bwa.sourceforge.net/
12
bd3a1e0de84c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
devteam
parents: 11
diff changeset
178
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
179 </token>
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
180 </macros>