Mercurial > repos > devteam > bwa

annotate bwa.xml @ 16:47c6967dc4e0 draft default tip

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 8f4d108191d52e3b60212dfcc3f57541e5f849d0
author iuc
date Fri, 19 Aug 2022 18:51:11 +0000
parents 22b497739c9c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
1 <?xml version="1.0"?>
16
47c6967dc4e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 8f4d108191d52e3b60212dfcc3f57541e5f849d0
iuc
parents: 15
diff changeset
2 <tool id="bwa" name="Map with BWA" version="@VERSION@.5">
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
3 <description>- map short reads (&lt; 100 bp) against reference genome</description>
15
22b497739c9c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 12
diff changeset
4 <xrefs>
22b497739c9c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 12
diff changeset
5 <xref type="bio.tools">bwa</xref>
22b497739c9c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 12
diff changeset
6 </xrefs>
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
7 <macros>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
8 <import>read_group_macros.xml</import>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
9 <import>bwa_macros.xml</import>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
10 <token name="@command_options@">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
11 #if str( $analysis_type.analysis_type_selector ) == "full":
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
12 -n ${analysis_type.n}
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
13 -o ${analysis_type.o}
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
14 -e ${analysis_type.e}
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
15 -i ${analysis_type.i}
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
16 -d ${analysis_type.d}
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
17 -l ${analysis_type.l}
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
18 -k ${analysis_type.k}
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
19 -m ${analysis_type.m}
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
20 -M ${analysis_type.M}
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
21 -O ${analysis_type.O}
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
22 -E ${analysis_type.E}
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
23 -R ${analysis_type.R}
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
24 -q ${analysis_type.q}
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
25 #if str( $analysis_type.B ):
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
26 -B ${analysis_type.B}
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
27 #end if
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
28 #if str( $analysis_type.L ):
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
29 -L ${analysis_type.L}
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
30 #end if
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
31 #end if
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
32 </token>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
33 <token name="@read_group_options@">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
34 #if $use_rg:
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
35 @set_rg_string@
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
36 -r '$rg_string'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
37 #end if
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
38 </token>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
39 <xml name="advanced_pe_options">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
40 <param name="adv_pe_options_selector" type="select" label="Set advanced paired end options?"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
41 help="Provides additional controls">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
42 <option value="set">Set</option>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
43 <option value="do_not_set" selected="True">Do not set</option>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
44 </param>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
45 <when value="set">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
46 <param name="a" type="integer" value="500"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
47 label="Maximum insert size for a read pair to be considered being mapped properly."
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
48 help="sampe -a; This option is only used when there are not enough good alignment to infer the distribution of insert sizes; default=500"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
49 <param name="o" type="integer" value="100000"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
50 label="Maximum occurrences of a read for pairing. A read with more occurrences will be treated as a single-end read."
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
51 help="sampe -o; Reducing this parameter helps faster pairing; default=100000"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
52 <param name="n" type="integer" value="3"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
53 label="Maximum number of alignments to output in the XA tag for reads paired properly."
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
54 help="sampe -n; If a read has more than this many hits, the XA tag will not be written; default=3"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
55 <param name="N" type="integer" value="10"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
56 label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons)."
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
57 help="sampe -N; If a read has more than this many hits, the XA tag will not be written; default=10"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
58 <param name="c" type="float" value="0.00005" label="Prior of chimeric rate (lower bound)"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
59 help="sampe -c"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
60 </when>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
61 <when value="do_not_set">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
62 <!-- do nothing -->
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
63 </when>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
64 </xml>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
65 <xml name="advanced_se_options">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
66 <param name="adv_se_options_selector" type="select" label="Set advanced single end options?"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
67 help="Provides additional controls">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
68 <option value="set">Set</option>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
69 <option value="do_not_set" selected="True">Do not set</option>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
70 </param>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
71 <when value="set">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
72 <param name="n" type="integer" value="3" label="Maximum number of alignments to output in the XA tag."
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
73 help="-n; If a read has more than this many hits, the XA tag will not be written; default=3"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
74 </when>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
75 <when value="do_not_set">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
76 <!-- do nothing -->
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
77 </when>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
78 </xml>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
79 </macros>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
80 <expand macro="requirements"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
81 <expand macro="stdio"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
82 <command>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
83 <![CDATA[
11
6def3ba376a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
iuc
parents: 10
diff changeset
84 @pipefail@
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
85 @set_reference_fasta_filename@
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
86
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
87 ## setup vars for rg handling...
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
88 @define_read_group_helpers@
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
89 #if str( $input_type.input_type_selector ) == "paired":
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
90 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1, $input_type.fastq_input2)
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
91 #elif str( $input_type.input_type_selector ) in ["single_bam", "paired_bam"]:
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
92 #set $rg_auto_name = $read_group_name_default($input_type.bam_input)
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
93 #else
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
94 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1)
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
95 #end if
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
96 @set_use_rg_var@
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
97 @set_read_group_vars@
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
98
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
99 ## Begin bwa command line
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
100
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
101 ####### Fastq paired
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
102
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
103 #if str( $input_type.input_type_selector ) == "paired" or str( $input_type.input_type_selector ) == "paired_collection":
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
104 bwa aln
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
105 -t "\${GALAXY_SLOTS:-1}"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
106 @command_options@
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
107 '$reference_fasta_filename'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
108 #if str( $input_type.input_type_selector ) == "paired_collection":
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
109 '${input_type.fastq_input1.forward}'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
110 #else
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
111 '${input_type.fastq_input1}'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
112 #end if
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
113 > first.sai &&
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
114
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
115 bwa aln
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
116 -t "\${GALAXY_SLOTS:-1}"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
117 @command_options@
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
118 '${reference_fasta_filename}'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
119 #if str( $input_type.input_type_selector ) == "paired_collection":
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
120 '${input_type.fastq_input1.reverse}'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
121 #else
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
122 '${input_type.fastq_input2}'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
123 #end if
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
124 > second.sai &&
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
125
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
126 bwa sampe
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
127 #if str( $input_type.adv_pe_options.adv_pe_options_selector) == "True":
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
128 -a ${$input_type.adv_pe_options.a}
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
129 -o ${$input_type.adv_pe_options.o}
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
130 -n ${$input_type.adv_pe_options.n}
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
131 -N ${$input_type.adv_pe_options.N}
16
47c6967dc4e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 8f4d108191d52e3b60212dfcc3f57541e5f849d0
iuc
parents: 15
diff changeset
132 -c ${$input_type.adv_pe_options.c}
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
133 #end if
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
134 @read_group_options@
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
135 #if str( $input_type.input_type_selector ) == "paired_collection":
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
136 '${reference_fasta_filename}' first.sai second.sai '${input_type.fastq_input1.forward}' '${input_type.fastq_input1.reverse}'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
137 #else:
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
138 '${reference_fasta_filename}' first.sai second.sai '${input_type.fastq_input1}' '${input_type.fastq_input2}'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
139 #end if
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
140
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
141 ## Fastq single
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
142
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
143 #elif str( $input_type.input_type_selector ) == "single":
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
144 bwa aln
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
145 -t "\${GALAXY_SLOTS:-1}"
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
146
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
147 @command_options@
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
148
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
149 '${reference_fasta_filename}'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
150 '${input_type.fastq_input1}'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
151 > first.sai &&
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
152
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
153 bwa samse
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
154
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
155 #if str( $input_type.adv_se_options.adv_se_options_selector) == "True":
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
156 -n ${$input_type.adv_se_options.n}
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
157 #end if
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
158 @read_group_options@
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
159 '${reference_fasta_filename}' first.sai '${input_type.fastq_input1}'
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
160
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
161 ####### BAM paired
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
162
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
163 #elif str( $input_type.input_type_selector ) == "paired_bam":
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
164 bwa aln
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
165 -t "\${GALAXY_SLOTS:-1}"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
166 -b
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
167 -1
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
168 @command_options@
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
169 '${reference_fasta_filename}'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
170 '${input_type.bam_input}'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
171 > first.sai &&
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
172
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
173 bwa aln
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
174 -t "\${GALAXY_SLOTS:-1}"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
175 -b
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
176 -2
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
177 @command_options@
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
178 '${reference_fasta_filename}'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
179 '${input_type.bam_input}'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
180 > second.sai &&
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
181
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
182 bwa sampe
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
183
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
184 #if str( $input_type.adv_bam_pe_options.adv_pe_options_selector) == "True":
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
185 -a ${$input_type.adv_bam_pe_options.a}
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
186 -o ${$input_type.adv_bam_pe_options.o}
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
187 -n ${$input_type.adv_bam_pe_options.n}
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
188 -N ${$input_type.adv_bam_pe_options.N}
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
189 #end if
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
190 @read_group_options@
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
191 '${reference_fasta_filename}' first.sai second.sai '${input_type.bam_input}' '${input_type.bam_input}'
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
192
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
193 ####### Fastq single ------------ to do next
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
194
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
195 #elif str( $input_type.input_type_selector ) == "single_bam":
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
196 bwa aln
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
197 -t "\${GALAXY_SLOTS:-1}"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
198 -b
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
199 -0
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
200
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
201 @command_options@
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
202
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
203 '${reference_fasta_filename}'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
204 '${input_type.bam_input}'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
205 > first.sai &&
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
206
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
207 bwa samse
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
208
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
209 #if str( $input_type.adv_bam_se_options.adv_se_options_selector) == "True":
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
210 -n ${$input_type.adv_bam_se_options.n}
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
211 #end if
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
212 @read_group_options@
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
213 '${reference_fasta_filename}' first.sai '${input_type.bam_input}'
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
214 #end if
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
215
12
086ba7b646e5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
iuc
parents: 11
diff changeset
216 | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
217 ]]>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
218 </command>
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
219
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
220 <inputs>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
221 <expand macro="reference_source_conditional"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
222 <conditional name="input_type">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
223 <param name="input_type_selector" type="select" label="Select input type"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
224 help="Select between fastq and bam datasets and between paired and single end data">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
225 <option value="paired">Paired fastq</option>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
226 <option value="paired_collection">Paired fastq collection</option>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
227 <option value="single">Single fastq</option>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
228 <option value="paired_bam">Paired BAM</option>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
229 <option value="single_bam">Single BAM</option>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
230 </param>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
231 <when value="paired">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
232 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
233 label="Select first set of reads" help="Specify dataset with forward reads"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
234 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
235 label="Select second set of reads" help="Specify dataset with reverse reads"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
236 <conditional name="adv_pe_options">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
237 <expand macro="advanced_pe_options"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
238 </conditional>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
239 </when>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
240 <when value="paired_collection">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
241 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
242 help="See help section for an explanation of dataset collections"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
243 <conditional name="adv_pe_options">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
244 <expand macro="advanced_pe_options"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
245 </conditional>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
246 </when>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
247 <when value="single">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
248 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
249 label="Select fastq dataset" help="Specify dataset with single reads"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
250 <conditional name="adv_se_options">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
251 <expand macro="advanced_se_options"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
252 </conditional>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
253 </when>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
254 <!-- the difference between single and paired bams is in the <command> tag portion and realated to -0, -1, and -2 options -->
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
255 <when value="paired_bam">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
256 <param name="bam_input" type="data" format="bam" label="Select BAM dataset"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
257 help="Specify BAM dataset with paired reads"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
258 <conditional name="adv_bam_pe_options">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
259 <expand macro="advanced_pe_options"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
260 </conditional>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
261 </when>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
262 <when value="single_bam">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
263 <param name="bam_input" type="data" format="bam" label="Select BAM dataset"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
264 help="Specify BAM dataset with single reads"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
265 <conditional name="adv_bam_se_options">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
266 <expand macro="advanced_se_options"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
267 </conditional>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
268 </when>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
269 </conditional>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
270 <expand macro="read_group_conditional"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
271 <conditional name="analysis_type">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
272 <param name="analysis_type_selector" type="select" label="Select analysis mode">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
273 <option value="illumina">1.Simple Illumina mode</option>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
274 <option value="full">2.Full list of options</option>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
275 </param>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
276 <when value="illumina">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
277 <!-- do nothing -->
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
278 </when>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
279 <when value="full">
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
280 <param name="n" type="text" value="0.04"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
281 label="maximum edit distance if the value is integer, or the fraction of missing alignments given 2% uniform base error rate if float. In the latter case, the maximum edit distance is automatically chosen for different read lengths."
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
282 help="aln -n; default=0.04"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
283 <param name="o" type="integer" value="1" label="maximum number or gap openings"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
284 help="aln -o; default=1"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
285 <param name="e" type="integer" value="-1" label="maximum number of gap extensions"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
286 help="aln -e; -1 disables long gaps and invokes k-difference mode; default=-1"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
287 <param name="i" type="integer" value="5"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
288 label="do not put an indel within this many bp towards the ends" help="aln -i; default=5"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
289 <param name="d" type="integer" value="10" label="maximum occurrences for extending a long deletion"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
290 help="aln -d; default=10"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
291 <param name="l" type="integer" value="32" label="seed length" help="aln -l; default=32"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
292 <param name="k" type="integer" value="2" label="maximum differences in the seed"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
293 help="aln -k; default=2"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
294 <param name="m" type="integer" value="2000000" label="maximum entries in the queue"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
295 help="aln -m; default=2000000"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
296 <param name="M" type="integer" value="3" label="mismatch penalty" help="aln -M; default=3"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
297 <param name="O" type="integer" value="11" label="gap open penalty" help="aln -O; default=11"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
298 <param name="E" type="integer" value="4" label="gap extension penalty" help="aln -E; default=4"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
299 <param name="R" type="integer" value="30"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
300 label="stop searching when there are more than this value of equally best hits"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
301 help="aln -R; default=30"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
302 <param name="q" type="integer" value="0" label="quality threshold for read trimming down to 35bp"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
303 help="aln -q; default=0"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
304 <param name="B" type="integer" optional="True" label="length of barcode"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
305 help="aln -B; optional parameter"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
306 <param name="L" type="float" optional="True" label="log-scaled gap penalty for long deletions"
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
307 help="aln -L; optional parameter"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
308 </when>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
309 </conditional>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
310 </inputs>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
311 <outputs>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
312 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
10
29299da15326 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 4a306ebd8b7808ce963a69a3b15dd860c1fde585
iuc
parents: 8
diff changeset
313 <expand macro="dbKeyActionsBwaMem"/>
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
314 </data>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
315 </outputs>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
316 <tests>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
317 <test>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
318 <param name="reference_source_selector" value="history"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
319 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
320 <param name="input_type_selector" value="single"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
321 <param name="fastq_input1" ftype="fasta" value="bwa-mem-fasta1.fa"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
322 <param name="analysis_type_selector" value="illumina"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
323 <output name="bam_output" ftype="bam" file="bwa-aln-test1-fasta.bam" lines_diff="2"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
324 </test>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
325 <test>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
326 <param name="reference_source_selector" value="history"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
327 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
328 <param name="input_type_selector" value="paired"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
329 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
330 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
331 <param name="analysis_type_selector" value="illumina"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
332 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
333 </test>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
334 <test>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
335 <param name="reference_source_selector" value="history"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
336 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
337 <param name="input_type_selector" value="paired"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
338 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
339 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
340 <param name="analysis_type_selector" value="illumina"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
341 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
342 </test>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
343 <test>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
344 <param name="reference_source_selector" value="history"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
345 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
346 <param name="input_type_selector" value="paired_bam"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
347 <param name="bam_input" ftype="bam" value="bwa-aln-bam-input.bam"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
348 <param name="analysis_type_selector" value="illumina"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
349 <output name="bam_output" ftype="bam" file="bwa-aln-test2.bam" lines_diff="2"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
350 </test>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
351 <test>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
352 <param name="reference_source_selector" value="history"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
353 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
354 <param name="input_type_selector" value="paired"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
355 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
356 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
357 <param name="rg_selector" value="set"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
358 <param name="ID" value="rg1"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
359 <param name="PL" value="CAPILLARY"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
360 <param name="analysis_type_selector" value="illumina"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
361 <output name="bam_output" ftype="bam" file="bwa-aln-test3.bam" lines_diff="2"/>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
362 </test>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
363 </tests>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
364 <help><![CDATA[
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
365 **What is does**
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
366
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
367 BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
368 human genome. The bwa-aln algorithm is designed for Illumina sequence reads up to 100bp. For longer reads use
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
369 the separate BWA-MEM Galaxy tool.
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
370
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
371 This Galaxy tool wraps bwa-aln, bwa-samse and -sampe modules of bwa read mapping tool:
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
372
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
373 - **bwa aln** - actual mapper placing reads onto the reference sequence
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
374 - **bwa samse** - post-processor converting suffix array coordinates into genome coordinates in SAM format for
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
375 single reads
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
376 - **bam sampe** - post-processor for paired reads
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
377
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
378
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
379 The Galaxy implementation takes fastq or BAM (unaligned BAM) datasets as input and produces output in BAM format,
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
380 which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard).
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
381
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
382 -----
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
383
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
384 **Indices: Selecting reference genomes for BWA**
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
385
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
386 The Galaxy wrapper for BWA allows you to select between precomputed and user-defined indices for reference genomes
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
387 using the **Will you select a reference genome from your history or use a built-in index?** select box.
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
388
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
389 This select box has two options:
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
390
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
391 1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
392 reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bwa index utility
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
393 and are ready to be mapped against.
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
394 2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
395 reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
396 current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
397 from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
398 mapping with `bwa aln`.
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
399
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
400
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
401 If your genome of interest is not listed here you have two choices:
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
402
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
403 1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
404 needs to be added
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
405 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
406 and build index** option.
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
407
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
408
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
409 @RG@
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
410
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
411 @info@
8
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
412 ]]></help>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
413 <citations>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
414 <citation type="doi">10.1093/bioinformatics/btp324</citation>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
415 <citation type="doi">10.1093/bioinformatics/btp698</citation>
cbc665adcde4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 4
diff changeset
416 </citations>
0
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
417 </tool>