Mercurial > repos > devteam > bwa

annotate bwa-mem.xml @ 24:64f11cf59c6e 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 055c6c3de6c9e0f219f5792f6580244815c1cd31"
author iuc
date Wed, 05 May 2021 18:22:08 +0000
parents 3fe632431b68
children e188dc7a68e6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
1 <?xml version="1.0"?>
24
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
2 <tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.2">
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
3 <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
4 <macros>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
5 <import>read_group_macros.xml</import>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
6 <import>bwa_macros.xml</import>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
7 </macros>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
8 <expand macro="requirements"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
9 <expand macro="stdio"/>
20
4f774c1e6049 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 4a306ebd8b7808ce963a69a3b15dd860c1fde585
iuc
parents: 18
diff changeset
10 <command><![CDATA[
21
8d2a528a9513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
iuc
parents: 20
diff changeset
11 @pipefail@
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
12 @set_reference_fasta_filename@
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
13
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
14 ## Begin BWA-MEM command line
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
15
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
16 bwa mem
24
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
17
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
18 #if str( $output_sort ) == "unsorted":
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
19 -t 1
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
20 #else
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
21 -t "\${GALAXY_SLOTS:-1}"
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
22 #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
23 ## Verbosity is set to 1 (errors only)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
24 -v 1
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
25
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
26 #if str( $fastq_input.fastq_input_selector ) == "paired_iv":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
27 ## For interleaved fastq files set -p option
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
28 -p
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
29 ## check that insert statistics is used
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
30 #if str( $fastq_input.iset_stats ):
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
31 -I '${fastq_input.iset_stats}'
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
32 #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
33 #end if
2
e29bc5c169bc Uploaded
devteam
parents: 1
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 #if str( $analysis_type.analysis_type_selector ) not in ["illumina", "full"]:
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
36 -x '$analysis_type.analysis_type_selector'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
37 #elif str( $analysis_type.analysis_type_selector ) == "full":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
38 ## Algorithmic options
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
39 #if str( $analysis_type.algorithmic_options.algorithmic_options_selector ) == "set":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
40 -k '${analysis_type.algorithmic_options.k}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
41 -w '${analysis_type.algorithmic_options.w}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
42 -d '${analysis_type.algorithmic_options.d}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
43 -r '${analysis_type.algorithmic_options.r}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
44 -y '${analysis_type.algorithmic_options.y}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
45 -c '${analysis_type.algorithmic_options.c}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
46 -D '${analysis_type.algorithmic_options.D}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
47 -W '${analysis_type.algorithmic_options.W}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
48 -m '${analysis_type.algorithmic_options.m}'
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
49 ${analysis_type.algorithmic_options.S}
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
50 ${analysis_type.algorithmic_options.P}
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
51 ${analysis_type.algorithmic_options.e}
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
52 #end if
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
53
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
54 ## Scoring options
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
55 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "set":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
56 -A '${analysis_type.scoring_options.A}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
57 -B '${analysis_type.scoring_options.B}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
58 -O '${analysis_type.scoring_options.O}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
59 -E '${analysis_type.scoring_options.E}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
60 -L '${analysis_type.scoring_options.L}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
61 -U '${analysis_type.scoring_options.U}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
62 #end if
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
63
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
64 ## IO options
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
65 #if str( $analysis_type.io_options.io_options_selector ) == "set":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
66 -T '${analysis_type.io_options.T}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
67 -h '${analysis_type.io_options.h}'
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
68 ${analysis_type.io_options.a}
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
69 ${analysis_type.io_options.C}
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
70 ${analysis_type.io_options.V}
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
71 ${analysis_type.io_options.Y}
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
72 ${analysis_type.io_options.M}
15
4d82cf59895e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit dead2eaab58698fe02b8bb068f8d859eba551e8d
devteam
parents: 14
diff changeset
73 ${analysis_type.io_options.five}
16
be4e38d127ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit e1191c87a0fccfafa0f23c3bd09f416a6700b387
devteam
parents: 15
diff changeset
74 ${analysis_type.io_options.q}
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
75 #end if
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
76
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
77 #end if
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
78
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
79 ## Handle read group options...
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
80 @define_read_group_helpers@
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
81 #if str( $fastq_input.fastq_input_selector ) == "paired":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
82 #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1, $fastq_input.fastq_input2)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
83 #else:
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
84 #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
85 #end if
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
86 @set_use_rg_var@
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
87 @set_read_group_vars@
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
88 #if $use_rg
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
89 @set_rg_string@
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
90 -R '$rg_string'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
91 #end if
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
92
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
93 #if str( $fastq_input.fastq_input_selector ) == "paired":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
94 ## check that insert statistics is used
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
95 #if str( $fastq_input.iset_stats ):
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
96 -I '${fastq_input.iset_stats}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
97 #end if
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
98
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
99 '${reference_fasta_filename}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
100 '${fastq_input.fastq_input1}' '${fastq_input.fastq_input2}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
101 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
102 ## check that insert statistics is used
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
103 #if str( $fastq_input.iset_stats ):
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
104 -I '${fastq_input.iset_stats}'
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
105 #end if
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
106
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
107 '${reference_fasta_filename}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
108 '${fastq_input.fastq_input1.forward}' '${fastq_input.fastq_input1.reverse}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
109 #else:
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
110 '${reference_fasta_filename}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
111 '${fastq_input.fastq_input1}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
112 #end if
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
113
24
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
114 #if str( $output_sort ) == "coordinate":
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
115 | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
116 #elif str( $output_sort ) == "name":
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
117 | samtools sort -n -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
118 #else
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
119 | samtools view -@ \${GALAXY_SLOTS:-2} -bS - -o '$bam_output'
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
120 #end if
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
121
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
122
20
4f774c1e6049 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 4a306ebd8b7808ce963a69a3b15dd860c1fde585
iuc
parents: 18
diff changeset
123 ]]></command>
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
124
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
125 <inputs>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
126 <expand macro="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
127 <conditional name="fastq_input">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
128 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
129 <option value="paired">Paired</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
130 <option value="single">Single</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
131 <option value="paired_collection">Paired Collection</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
132 <option value="paired_iv">Paired Interleaved</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
133 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
134 <when value="paired">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
135 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
136 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
137 <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
138 <sanitizer invalid_char="">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
139 <valid initial="string.digits"><add value=","/> </valid>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
140 </sanitizer>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
141 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
142 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
143 <when value="single">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
144 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
145 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
146 <when value="paired_collection">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
147 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
148 <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
149 <sanitizer invalid_char="">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
150 <valid initial="string.digits"><add value=","/> </valid>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
151 </sanitizer>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
152 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
153 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
154 <when value="paired_iv">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
155 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
156 <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
157 <sanitizer invalid_char="">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
158 <valid initial="string.digits"><add value=","/> </valid>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
159 </sanitizer>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
160 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
161 </when>
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
162 </conditional>
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
163
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
164 <expand macro="read_group_conditional" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
165
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
166 <conditional name="analysis_type">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
167 <param name="analysis_type_selector" type="select" label="Select analysis mode">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
168 <option value="illumina">1.Simple Illumina mode</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
169 <option value="pacbio">2.PacBio mode (-x pacbio)</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
170 <option value="ont2d">3.Nanopore 2D-reads mode (-x ont2d)</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
171 <option value="intractg">4.Intra-species contigs mode (-x intractg)</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
172 <option value="full">5.Full list of options</option>
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
173 </param>
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
174 <when value="illumina">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
175 <!-- do nothing -->
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
176 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
177 <when value="pacbio">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
178 <!-- do nothing. all magic happens within <command> tag -->
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
179 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
180 <when value="ont2d">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
181 <!-- do nothing. all magic happens within <command> tag -->
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
182 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
183 <when value="intractg">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
184 <!-- do nothing. all magic happens within <command> tag -->
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
185 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
186 <when value="full">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
187 <conditional name="algorithmic_options">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
188 <param name="algorithmic_options_selector" type="select" label="Set algorithmic options?" help="Sets -k, -w, -d, -r, -y, -c, -D, -W, -m, -S, -P, and -e options.">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
189 <option value="set">Set</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
190 <option value="do_not_set" selected="True">Do not set</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
191 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
192 <when value="set">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
193 <param name="k" type="integer" value="19" label="Minimum seed length" help="-k; default=19"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
194 <param name="w" type="integer" value="100" label="Band width for banded alignment" help="-w; default=100"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
195 <param name="d" type="integer" value="100" label="Off-diagonal X-dropoff" help="-d; default=100"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
196 <param name="r" type="float" value="1.5" label="Look for internal seeds inside a seed longer than -k * THIS VALUE" help="-r; default=1.5; This is a key heuristic parameter for tuning the performance. Larger value yields fewer seeds, which leads to faster alignment speed but lower accuracy" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
197 <param name="y" type="integer" value="20" label="Seed occurrence for the 3rd round seeding" help="-y; default=20" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
198 <param name="c" type="integer" value="500" label="Skip seeds with more than that many occurrences" help="-c; default=500"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
199 <param name="D" type="float" value="0.5" label="Drop chains shorter than this fraction of the longest overlapping chain" help="-D; default=0.5"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
200 <param name="W" type="integer" value="0" label="Discard a chain if seeded bases shorter than THIS VALUE" help="-W; default=0"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
201 <param name="m" type="integer" value="50" label="Perform at most this many rounds of mate rescues for each read" help="-m; default=50"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
202 <param name="S" type="boolean" truevalue="-S" falsevalue="" label="Skip mate rescue" help="-S"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
203 <param name="P" type="boolean" truevalue="-P" falsevalue="" label="Skip pairing; mate rescue performed unless -S also in use" help="-P"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
204 <param name="e" type="boolean" truevalue="-e" falsevalue="" label="Discard full-length exact matches" help="-e"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
205 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
206 <when value="do_not_set">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
207 <!-- do nothing -->
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
208 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
209 </conditional>
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
210
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
211 <conditional name="scoring_options">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
212 <param name="scoring_options_selector" type="select" label="Set scoring options?" help="Sets -A, -B, -O, -E, -L, and -U options.">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
213 <option value="set">Set</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
214 <option value="do_not_set" selected="True">Do not set</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
215 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
216 <when value="set">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
217 <param name="A" type="integer" value="1" label="Score for a sequence match" help="-A; scales options -T, -d, -B, -O, -E, -L, and -U unless overridden; default=1"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
218 <param name="B" type="integer" value="4" label="Penalty for a mismatch" help="-B; default=4"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
219 <param name="O" type="text" value="6,6" label="Gap open penalties for deletions and insertions" help="-O; default=6,6">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
220 <sanitizer invalid_char="">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
221 <valid initial="string.digits"><add value=","/> </valid>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
222 </sanitizer>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
223 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
224 <param name="E" type="text" value="1,1" label="Gap extension penalties; a gap of size k cost &#39;-O + -E*k&#39;. If two numbers are specified, the first is the penalty of extending a deletion and the second for extending an insertion" help="-E; default=1,1">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
225 <sanitizer invalid_char="">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
226 <valid initial="string.digits"><add value=","/> </valid>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
227 </sanitizer>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
228 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
229 <param name="L" type="text" value="5,5" label="Penalties for 5&#39;-end and 3&#39;-end clipping" help="-L; default=5,5; When performing Smith-Waterman extension, BWA-MEM keeps track of the best score reaching the end of query. If this score is larger than the best Smith-Waterman score minus the clipping penalty, clipping will not be applied. Note that in this case, the SAM AS tag reports the best Smith-Waterman score; clipping penalty is not deduced">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
230 <sanitizer invalid_char="">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
231 <valid initial="string.digits"><add value=","/> </valid>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
232 </sanitizer>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
233 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
234 <param name="U" type="integer" value="17" label="Penalty for an unpaired read pair" help="-U; default=17"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
235 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
236 <when value="do_not_set">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
237 <!-- do nothing -->
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
238 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
239 </conditional>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
240
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
241 <conditional name="io_options">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
242 <param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, and -M options.">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
243 <option value="set">Set</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
244 <option value="do_not_set" selected="True">Do not set</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
245 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
246 <when value="set">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
247 <param name="five" argument="-5" type="boolean" truevalue="-5" falsevalue="" label="For split alignment, take alignment with smallest coordinate as primary" help="Useful for HiC data"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
248 <param argument="-q" type="boolean" truevalue="-q" falsevalue="" label="Don't lower MAPQ for split alignment" help="By default the MAPQ score of a supplementary alignment will be lowered to the primary alignment score."/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
249 <param name="T" type="integer" value="30" label="Minimum score to output" help="-T; default=30"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
250 <param name="h" type="integer" value="5" label="If there are less than THIS VALUE hits with score &gt;80% of the max score, output them all in the XA tag" help="-h; default=5" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
251 <param name="a" type="boolean" truevalue="-a" falsevalue="" label="Output all alignments for single-ends or unpaired paired-ends" help="-a; These alignments will be flagged as secondary alignments"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
252 <param name="C" type="boolean" truevalue="-C" falsevalue="" label="Append FASTA/FASTQ comment to BAM output" help="-C"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
253 <param name="V" type="boolean" truevalue="-V" falsevalue="" label="Output the reference FASTA header in the XR tag" help="-C"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
254 <param name="Y" type="boolean" truevalue="-Y" falsevalue="" label="Use soft clipping for supplementary alignments" help="-Y; By default, BWA-MEM uses soft clipping for the primary alignment and hard clipping for supplementary alignments" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
255 <param name="M" type="boolean" truevalue="-M" falsevalue="" label="Mark shorter split hits of a chimeric alignment in the FLAG field as 'secondary alignment' instead of 'supplementary alignment'" help="-M; For Picard&lt;1.96 compatibility" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
256 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
257 <when value="do_not_set">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
258 <!-- do nothing -->
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
259 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
260 </conditional>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
261 </when>
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
262 </conditional>
24
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
263 <param name="output_sort" type="select" label="BAM sorting mode" help="The 'Not sorted' option can extend the run time of the tool significantly (cause it requires running on only a single thread).">
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
264 <option value="coordinate" selected="True">Sort by chromosomal coordinates</option>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
265 <option value="name">Sort by read names (i.e., the QNAME field) </option>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
266 <option value="unsorted">Not sorted (sorted as input)</option>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
267 </param>
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
268 </inputs>
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
269
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
270 <outputs>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
271 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
272 <expand macro="dbKeyActionsBwaMem" />
24
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
273 <change_format>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
274 <when input="output_sort" value="name" format="qname_sorted.bam" />
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
275 <when input="output_sort" value="unsorted" format="qname_input_sorted.bam" />
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
276 </change_format>
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
277 </data>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
278 </outputs>
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
279
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
280 <tests>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
281 <test>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
282 <param name="reference_source_selector" value="history" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
283 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
284 <param name="fastq_input_selector" value="paired"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
285 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
286 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
287 <param name="analysis_type_selector" value="illumina"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
288 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="2" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
289 </test>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
290 <test>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
291 <param name="reference_source_selector" value="history" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
292 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
293 <param name="fastq_input_selector" value="single"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
294 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
295 <param name="analysis_type_selector" value="illumina"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
296 <output name="bam_output" ftype="bam" file="bwa-mem-test1-fasta.bam" lines_diff="2" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
297 </test>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
298 <test>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
299 <param name="reference_source_selector" value="history" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
300 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
301 <param name="fastq_input_selector" value="paired"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
302 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
303 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
304 <param name="analysis_type_selector" value="illumina"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
305 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="2" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
306 </test>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
307 <test>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
308 <param name="reference_source_selector" value="history" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
309 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
310 <param name="index_a" value="is"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
311 <param name="fastq_input_selector" value="paired"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
312 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
313 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
314 <param name="rg_selector" value="set"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
315 <param name="ID" value="rg1"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
316 <param name="PL" value="CAPILLARY"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
317 <param name="LB" value="AARDVARK-1" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
318 <param name="analysis_type_selector" value="illumina"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
319 <output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="2" />
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
320 </test>
24
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
321 <test>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
322 <param name="reference_source_selector" value="history" />
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
323 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
324 <param name="fastq_input_selector" value="paired"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
325 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
326 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
327 <param name="analysis_type_selector" value="illumina"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
328 <param name="output_sort" value="unsorted"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
329 <output name="bam_output" ftype="qname_input_sorted.bam" file="bwa-mem-test3.bam" lines_diff="2" />
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
330 </test>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
331 <test>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
332 <param name="reference_source_selector" value="history" />
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
333 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
334 <param name="fastq_input_selector" value="paired"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
335 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
336 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
337 <param name="analysis_type_selector" value="illumina"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
338 <param name="output_sort" value="name"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
339 <output name="bam_output" ftype="qname_sorted.bam" file="bwa-mem-test4.bam" lines_diff="2" />
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
340 </test>
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
341 </tests>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
342 <help><![CDATA[
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
343 **What is does**
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
344
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
345 From http://arxiv.org/abs/1303.3997:
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
346
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
347 BWA-MEM is an alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human.
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
348 It automatically chooses between local and end-to-end alignments, supports paired-end reads and performs chimeric alignment.
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
349 The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases.
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
350
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
351 This Galaxy tool wraps bwa-mem module of bwa read mapping tool. The Galaxy implementation takes fastq files as input and produces output in BAM format, which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard).
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
352
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
353 -----
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
354
4
ac30bfd3e2a8 planemo upload commit a50a3947aebc8a1d11bac39599f4efd8ed9a3bd5
devteam
parents: 2
diff changeset
355 **Indices: Selecting reference genomes for BWA**
ac30bfd3e2a8 planemo upload commit a50a3947aebc8a1d11bac39599f4efd8ed9a3bd5
devteam
parents: 2
diff changeset
356
ac30bfd3e2a8 planemo upload commit a50a3947aebc8a1d11bac39599f4efd8ed9a3bd5
devteam
parents: 2
diff changeset
357 Galaxy wrapper for BWA allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:
ac30bfd3e2a8 planemo upload commit a50a3947aebc8a1d11bac39599f4efd8ed9a3bd5
devteam
parents: 2
diff changeset
358
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
359 1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bwa index utility and are ready to be mapped against.
4
ac30bfd3e2a8 planemo upload commit a50a3947aebc8a1d11bac39599f4efd8ed9a3bd5
devteam
parents: 2
diff changeset
360 2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run mapping with `bwa mem`.
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
361
4
ac30bfd3e2a8 planemo upload commit a50a3947aebc8a1d11bac39599f4efd8ed9a3bd5
devteam
parents: 2
diff changeset
362 If your genome of interest is not listed here you have two choices:
ac30bfd3e2a8 planemo upload commit a50a3947aebc8a1d11bac39599f4efd8ed9a3bd5
devteam
parents: 2
diff changeset
363
ac30bfd3e2a8 planemo upload commit a50a3947aebc8a1d11bac39599f4efd8ed9a3bd5
devteam
parents: 2
diff changeset
364 1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added
ac30bfd3e2a8 planemo upload commit a50a3947aebc8a1d11bac39599f4efd8ed9a3bd5
devteam
parents: 2
diff changeset
365 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.
ac30bfd3e2a8 planemo upload commit a50a3947aebc8a1d11bac39599f4efd8ed9a3bd5
devteam
parents: 2
diff changeset
366
ac30bfd3e2a8 planemo upload commit a50a3947aebc8a1d11bac39599f4efd8ed9a3bd5
devteam
parents: 2
diff changeset
367 -----
ac30bfd3e2a8 planemo upload commit a50a3947aebc8a1d11bac39599f4efd8ed9a3bd5
devteam
parents: 2
diff changeset
368
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
369 **Galaxy-specific option**
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
370
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
371 Galaxy allows four levels of control over bwa-mem options provided by **Select analysis mode** menu option. These are:
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
372
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
373 1. *Simple Illumina mode*: The simplest possible bwa mem application in which it alignes single or paired-end data to reference using default parameters. It is equivalent to the following command: bwa mem <reference index> <fastq dataset1> [fastq dataset2]
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
374 2. *PacBio mode*: The mode adjusted specifically for mapping of long PacBio subreads. Equivalent to the following command: bwa mem -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 <reference index> <PacBio dataset in fastq format>
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
375 3. *Full list of options*: Allows access to all options through Galaxy interface.
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
376
24
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
377 -----
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
378
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
379 **Bam sorting mode**
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
380
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
381 The generated bam files can be sorted according to three criteria: coordinates, names and input order.
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
382
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
383 In coordinate sorted mode the reads are sorted by coordinates. It means that the reads from the beginning of the first chromosome are first in the file.
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
384
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
385 When sorted by read name, the file is sorted by the reference ID (i.e., the QNAME field).
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
386
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
387 Finally, the *No sorted (sorted as input)* option yield a BAM file in which the records are sorted in an order corresponding to the order of the reads in the original input file. This option requires using a single thread to perform the conversion from SAM to BAM format, so the runtime is extended.
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
388
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
iuc
parents: 23
diff changeset
389
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
390 @RG@
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
391
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
392 @info@
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
393 ]]></help>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
394 <citations>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
395 <citation type="doi">10.1093/bioinformatics/btp324</citation>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
396 <citation type="doi">10.1093/bioinformatics/btp698</citation>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
397 <citation type="bibtex">@misc{1303.3997,
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
398 Author = {Heng Li},
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
399 Title = {Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM},
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
400 Year = {2013},
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
401 Eprint = {arXiv:1303.3997},
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
402 url = {http://arxiv.org/abs/1303.3997},
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
403 }</citation>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 16
diff changeset
404 </citations>
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
405 </tool>