Mercurial > repos > devteam > bwa

annotate bwa.xml @ 26:2477830927ec 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 6e9628b1d92fdb358b79959ad54a456cfa46fa33
author iuc
date Fri, 17 May 2024 21:09:07 +0000
parents e188dc7a68e6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
1 <?xml version="1.0"?>
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
2 <tool id="bwa" name="Map with BWA" version="@TOOL_VERSION@" profile="22.05">
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
3 <description>- map short reads (&lt; 100 bp) against reference genome</description>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
4 <macros>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
5 <import>read_group_macros.xml</import>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
6 <import>bwa_macros.xml</import>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
7 <token name="@command_options@">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
8 #if str( $analysis_type.analysis_type_selector ) == "full":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
9 -n ${analysis_type.n}
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
10 -o ${analysis_type.o}
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
11 -e ${analysis_type.e}
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
12 -i ${analysis_type.i}
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
13 -d ${analysis_type.d}
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
14 -l ${analysis_type.l}
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
15 -k ${analysis_type.k}
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
16 -m ${analysis_type.m}
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
17 -M ${analysis_type.M}
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
18 -O ${analysis_type.O}
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
19 -E ${analysis_type.E}
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
20 -R ${analysis_type.R}
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
21 -q ${analysis_type.q}
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
22 #if str( $analysis_type.B ):
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
23 -B ${analysis_type.B}
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
24 #end if
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
25 #if str( $analysis_type.L ):
4
ac30bfd3e2a8 planemo upload commit a50a3947aebc8a1d11bac39599f4efd8ed9a3bd5
devteam
parents: 3
diff changeset
26 -L ${analysis_type.L}
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
27 #end if
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
28 #end if
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
29 </token>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
30 <token name="@read_group_options@">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
31 #if $use_rg:
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
32 @set_rg_string@
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
33 -r '$rg_string'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
34 #end if
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
35 </token>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
36 <xml name="advanced_pe_options">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
37 <param name="adv_pe_options_selector" type="select" label="Set advanced paired end options?"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
38 help="Provides additional controls">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
39 <option value="set">Set</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
40 <option value="do_not_set" selected="True">Do not set</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
41 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
42 <when value="set">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
43 <param name="a" type="integer" value="500"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
44 label="Maximum insert size for a read pair to be considered being mapped properly."
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
45 help="sampe -a; This option is only used when there are not enough good alignment to infer the distribution of insert sizes; default=500"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
46 <param name="o" type="integer" value="100000"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
47 label="Maximum occurrences of a read for pairing. A read with more occurrences will be treated as a single-end read."
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
48 help="sampe -o; Reducing this parameter helps faster pairing; default=100000"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
49 <param name="n" type="integer" value="3"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
50 label="Maximum number of alignments to output in the XA tag for reads paired properly."
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
51 help="sampe -n; If a read has more than this many hits, the XA tag will not be written; default=3"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
52 <param name="N" type="integer" value="10"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
53 label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons)."
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
54 help="sampe -N; If a read has more than this many hits, the XA tag will not be written; default=10"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
55 <param name="c" type="float" value="0.00005" label="Prior of chimeric rate (lower bound)"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
56 help="sampe -c"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
57 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
58 <when value="do_not_set">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
59 <!-- do nothing -->
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
60 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
61 </xml>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
62 <xml name="advanced_se_options">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
63 <param name="adv_se_options_selector" type="select" label="Set advanced single end options?"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
64 help="Provides additional controls">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
65 <option value="set">Set</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
66 <option value="do_not_set" selected="True">Do not set</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
67 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
68 <when value="set">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
69 <param name="n" type="integer" value="3" label="Maximum number of alignments to output in the XA tag."
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
70 help="-n; If a read has more than this many hits, the XA tag will not be written; default=3"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
71 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
72 <when value="do_not_set">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
73 <!-- do nothing -->
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
74 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
75 </xml>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
76 </macros>
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
77 <expand macro="bio_tools"/>
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
78 <expand macro="requirements"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
79 <expand macro="stdio"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
80 <command>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
81 <![CDATA[
21
8d2a528a9513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
iuc
parents: 20
diff changeset
82 @pipefail@
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
83 @set_reference_fasta_filename@
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
84
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
85 ## setup vars for rg handling...
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
86 @define_read_group_helpers@
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
87 #if str( $input_type.input_type_selector ) == "paired":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
88 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1, $input_type.fastq_input2)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
89 #elif str( $input_type.input_type_selector ) in ["single_bam", "paired_bam"]:
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
90 #set $rg_auto_name = $read_group_name_default($input_type.bam_input)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
91 #else
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
92 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1)
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
93 #end if
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
94 @set_use_rg_var@
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
95 @set_read_group_vars@
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
96
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
97 ## Begin bwa command line
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
98
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
99 ####### Fastq paired
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
100
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
101 #if str( $input_type.input_type_selector ) == "paired" or str( $input_type.input_type_selector ) == "paired_collection":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
102 bwa aln
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
103 -t "\${GALAXY_SLOTS:-1}"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
104 @command_options@
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
105 '$reference_fasta_filename'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
106 #if str( $input_type.input_type_selector ) == "paired_collection":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
107 '${input_type.fastq_input1.forward}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
108 #else
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
109 '${input_type.fastq_input1}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
110 #end if
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
111 > first.sai &&
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
112
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
113 bwa aln
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
114 -t "\${GALAXY_SLOTS:-1}"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
115 @command_options@
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
116 '${reference_fasta_filename}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
117 #if str( $input_type.input_type_selector ) == "paired_collection":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
118 '${input_type.fastq_input1.reverse}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
119 #else
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
120 '${input_type.fastq_input2}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
121 #end if
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
122 > second.sai &&
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
123
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
124 bwa sampe
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
125 #if str( $input_type.adv_pe_options.adv_pe_options_selector) == "True":
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
126 -a ${$input_type.adv_pe_options.a}
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
127 -o ${$input_type.adv_pe_options.o}
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
128 -n ${$input_type.adv_pe_options.n}
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
129 -N ${$input_type.adv_pe_options.N}
25
e188dc7a68e6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 8f4d108191d52e3b60212dfcc3f57541e5f849d0
iuc
parents: 23
diff changeset
130 -c ${$input_type.adv_pe_options.c}
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
131 #end if
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
132 @read_group_options@
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
133 #if str( $input_type.input_type_selector ) == "paired_collection":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
134 '${reference_fasta_filename}' first.sai second.sai '${input_type.fastq_input1.forward}' '${input_type.fastq_input1.reverse}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
135 #else:
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
136 '${reference_fasta_filename}' first.sai second.sai '${input_type.fastq_input1}' '${input_type.fastq_input2}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
137 #end if
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
138
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
139 ## Fastq single
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
140
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
141 #elif str( $input_type.input_type_selector ) == "single":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
142 bwa aln
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
143 -t "\${GALAXY_SLOTS:-1}"
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
144
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
145 @command_options@
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
146
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
147 '${reference_fasta_filename}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
148 '${input_type.fastq_input1}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
149 > first.sai &&
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
150
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
151 bwa samse
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
152
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
153 #if str( $input_type.adv_se_options.adv_se_options_selector) == "True":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
154 -n ${$input_type.adv_se_options.n}
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
155 #end if
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
156 @read_group_options@
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
157 '${reference_fasta_filename}' first.sai '${input_type.fastq_input1}'
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
158
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
159 ####### BAM paired
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
160
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
161 #elif str( $input_type.input_type_selector ) == "paired_bam":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
162 bwa aln
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
163 -t "\${GALAXY_SLOTS:-1}"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
164 -b
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
165 -1
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
166 @command_options@
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
167 '${reference_fasta_filename}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
168 '${input_type.bam_input}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
169 > first.sai &&
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
170
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
171 bwa aln
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
172 -t "\${GALAXY_SLOTS:-1}"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
173 -b
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
174 -2
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
175 @command_options@
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
176 '${reference_fasta_filename}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
177 '${input_type.bam_input}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
178 > second.sai &&
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
179
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
180 bwa sampe
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
181
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
182 #if str( $input_type.adv_bam_pe_options.adv_pe_options_selector) == "True":
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
183 -a ${$input_type.adv_bam_pe_options.a}
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
184 -o ${$input_type.adv_bam_pe_options.o}
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
185 -n ${$input_type.adv_bam_pe_options.n}
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
186 -N ${$input_type.adv_bam_pe_options.N}
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
187 #end if
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
188 @read_group_options@
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
189 '${reference_fasta_filename}' first.sai second.sai '${input_type.bam_input}' '${input_type.bam_input}'
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
190
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
191 ####### Fastq single ------------ to do next
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
192
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
193 #elif str( $input_type.input_type_selector ) == "single_bam":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
194 bwa aln
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
195 -t "\${GALAXY_SLOTS:-1}"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
196 -b
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
197 -0
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
198
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
199 @command_options@
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
200
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
201 '${reference_fasta_filename}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
202 '${input_type.bam_input}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
203 > first.sai &&
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
204
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
205 bwa samse
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
206
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
207 #if str( $input_type.adv_bam_se_options.adv_se_options_selector) == "True":
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
208 -n ${$input_type.adv_bam_se_options.n}
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
209 #end if
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
210 @read_group_options@
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
211 '${reference_fasta_filename}' first.sai '${input_type.bam_input}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
212 #end if
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
213
23
3fe632431b68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 777181bd04849dab271ee2cc95e45c182947d308"
iuc
parents: 21
diff changeset
214 | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
215 ]]>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
216 </command>
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
217
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
218 <inputs>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
219 <expand macro="reference_source_conditional"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
220 <conditional name="input_type">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
221 <param name="input_type_selector" type="select" label="Select input type"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
222 help="Select between fastq and bam datasets and between paired and single end data">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
223 <option value="paired">Paired fastq</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
224 <option value="paired_collection">Paired fastq collection</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
225 <option value="single">Single fastq</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
226 <option value="paired_bam">Paired BAM</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
227 <option value="single_bam">Single BAM</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
228 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
229 <when value="paired">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
230 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
231 label="Select first set of reads" help="Specify dataset with forward reads"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
232 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
233 label="Select second set of reads" help="Specify dataset with reverse reads"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
234 <conditional name="adv_pe_options">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
235 <expand macro="advanced_pe_options"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
236 </conditional>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
237 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
238 <when value="paired_collection">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
239 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
240 help="See help section for an explanation of dataset collections"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
241 <conditional name="adv_pe_options">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
242 <expand macro="advanced_pe_options"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
243 </conditional>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
244 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
245 <when value="single">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
246 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
247 label="Select fastq dataset" help="Specify dataset with single reads"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
248 <conditional name="adv_se_options">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
249 <expand macro="advanced_se_options"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
250 </conditional>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
251 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
252 <!-- the difference between single and paired bams is in the <command> tag portion and realated to -0, -1, and -2 options -->
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
253 <when value="paired_bam">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
254 <param name="bam_input" type="data" format="bam" label="Select BAM dataset"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
255 help="Specify BAM dataset with paired reads"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
256 <conditional name="adv_bam_pe_options">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
257 <expand macro="advanced_pe_options"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
258 </conditional>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
259 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
260 <when value="single_bam">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
261 <param name="bam_input" type="data" format="bam" label="Select BAM dataset"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
262 help="Specify BAM dataset with single reads"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
263 <conditional name="adv_bam_se_options">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
264 <expand macro="advanced_se_options"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
265 </conditional>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
266 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
267 </conditional>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
268 <expand macro="read_group_conditional"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
269 <conditional name="analysis_type">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
270 <param name="analysis_type_selector" type="select" label="Select analysis mode">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
271 <option value="illumina">1.Simple Illumina mode</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
272 <option value="full">2.Full list of options</option>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
273 </param>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
274 <when value="illumina">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
275 <!-- do nothing -->
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
276 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
277 <when value="full">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
278 <param name="n" type="text" value="0.04"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
279 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."
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
280 help="aln -n; default=0.04"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
281 <param name="o" type="integer" value="1" label="maximum number or gap openings"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
282 help="aln -o; default=1"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
283 <param name="e" type="integer" value="-1" label="maximum number of gap extensions"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
284 help="aln -e; -1 disables long gaps and invokes k-difference mode; default=-1"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
285 <param name="i" type="integer" value="5"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
286 label="do not put an indel within this many bp towards the ends" help="aln -i; default=5"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
287 <param name="d" type="integer" value="10" label="maximum occurrences for extending a long deletion"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
288 help="aln -d; default=10"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
289 <param name="l" type="integer" value="32" label="seed length" help="aln -l; default=32"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
290 <param name="k" type="integer" value="2" label="maximum differences in the seed"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
291 help="aln -k; default=2"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
292 <param name="m" type="integer" value="2000000" label="maximum entries in the queue"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
293 help="aln -m; default=2000000"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
294 <param name="M" type="integer" value="3" label="mismatch penalty" help="aln -M; default=3"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
295 <param name="O" type="integer" value="11" label="gap open penalty" help="aln -O; default=11"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
296 <param name="E" type="integer" value="4" label="gap extension penalty" help="aln -E; default=4"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
297 <param name="R" type="integer" value="30"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
298 label="stop searching when there are more than this value of equally best hits"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
299 help="aln -R; default=30"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
300 <param name="q" type="integer" value="0" label="quality threshold for read trimming down to 35bp"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
301 help="aln -q; default=0"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
302 <param name="B" type="integer" optional="True" label="length of barcode"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
303 help="aln -B; optional parameter"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
304 <param name="L" type="float" optional="True" label="log-scaled gap penalty for long deletions"
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
305 help="aln -L; optional parameter"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
306 </when>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
307 </conditional>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
308 </inputs>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
309 <outputs>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
310 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
20
4f774c1e6049 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 4a306ebd8b7808ce963a69a3b15dd860c1fde585
iuc
parents: 18
diff changeset
311 <expand macro="dbKeyActionsBwaMem"/>
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
312 </data>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
313 </outputs>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
314 <tests>
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
315 <!-- `samtools sort` in the new update adds PG lines to the output so the lines_diff is changed from "2" to "4" -->
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
316 <test expect_num_outputs="1">
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
317 <param name="reference_source_selector" value="history"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
318 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
319 <param name="input_type_selector" value="single"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
320 <param name="fastq_input1" ftype="fasta" value="bwa-mem-fasta1.fa"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
321 <param name="analysis_type_selector" value="illumina"/>
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
322 <output name="bam_output" ftype="bam" file="bwa-aln-test1-fasta.bam" lines_diff="4"/>
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
323 </test>
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
324 <test expect_num_outputs="1">
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
325 <param name="reference_source_selector" value="history"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
326 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
327 <param name="input_type_selector" value="paired"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
328 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
329 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
330 <param name="analysis_type_selector" value="illumina"/>
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
331 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="4"/>
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
332 </test>
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
333 <test expect_num_outputs="1">
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
334 <param name="reference_source_selector" value="history"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
335 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
336 <param name="input_type_selector" value="paired"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
337 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
338 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
339 <param name="analysis_type_selector" value="illumina"/>
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
340 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="4"/>
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
341 </test>
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
342 <test expect_num_outputs="1">
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
343 <param name="reference_source_selector" value="history"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
344 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
345 <param name="input_type_selector" value="paired_bam"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
346 <param name="bam_input" ftype="bam" value="bwa-aln-bam-input.bam"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
347 <param name="analysis_type_selector" value="illumina"/>
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
348 <output name="bam_output" ftype="bam" file="bwa-aln-test2.bam" lines_diff="4"/>
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
349 </test>
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
350 <test expect_num_outputs="1">
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
351 <param name="reference_source_selector" value="history"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
352 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
353 <param name="input_type_selector" value="paired"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
354 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
355 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
356 <param name="rg_selector" value="set"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
357 <param name="ID" value="rg1"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
358 <param name="PL" value="CAPILLARY"/>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
359 <param name="analysis_type_selector" value="illumina"/>
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
360 <output name="bam_output" ftype="bam" file="bwa-aln-test3.bam" lines_diff="5"/>
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
361 </test>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
362 </tests>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
363 <help><![CDATA[
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
364 **What it does**
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
365
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
366 BWA_ is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
367 The bwa-aln algorithm is designed for Illumina sequence reads up to 100bp. For longer reads use the separate BWA-MEM Galaxy tool.
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
368
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
369 This Galaxy tool wraps the bwa-aln, bwa-samse and -sampe modules of the BWA read mapping tool:
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
370
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
371 - **bwa aln** - actual mapper placing reads onto the reference sequence
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
372 - **bwa samse** - post-processor converting suffix array coordinates into genome coordinates in SAM format for
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
373 single reads
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
374 - **bam sampe** - post-processor for paired reads
2
e29bc5c169bc Uploaded
devteam
parents: 1
diff changeset
375
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
376 For more details about the different modules of the BWA package see the `BWA manual`_.
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
377
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
378 The Galaxy implementation takes fastq or BAM (unaligned BAM) datasets as input and produces output in BAM format,
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
379 which can be further processed using various BAM utilities existing in Galaxy (BAMTools, SAMTools, Picard).
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
380
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
381 -----
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
382
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
383 @ref_genomes@
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
384
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
385 @RG@
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
386
26
2477830927ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
iuc
parents: 25
diff changeset
387 @links@
18
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
388 ]]></help>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
389 <citations>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
390 <citation type="doi">10.1093/bioinformatics/btp324</citation>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
391 <citation type="doi">10.1093/bioinformatics/btp698</citation>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
iuc
parents: 14
diff changeset
392 </citations>
0
ff1ae217ccc2 Uploaded
devteam
parents:
diff changeset
393 </tool>