annotate bowtie2_wrapper.xml @ 9:019c2a81547a draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 07975ea169793d7d072439ce0cf8f773e1f06177
author devteam
date Wed, 18 Nov 2015 09:51:30 -0500
parents 82414e16b6bd
children a9d4f71dbfb0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
82414e16b6bd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 637e614b544bf3cd75306f27bcfe537cacae4a58
devteam
parents: 7
diff changeset
1 <tool id="bowtie2" name="Bowtie2" version="2.2.6">
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
2 <description>- map reads against reference genome</description>
5
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
3 <macros>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
4 <import>read_group_macros.xml</import>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
5 </macros>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
6 <version_command>bowtie2 --version</version_command>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
7 <requirements>
8
82414e16b6bd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 637e614b544bf3cd75306f27bcfe537cacae4a58
devteam
parents: 7
diff changeset
8 <requirement type="package" version="2.2.6">bowtie2</requirement>
82414e16b6bd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 637e614b544bf3cd75306f27bcfe537cacae4a58
devteam
parents: 7
diff changeset
9 <requirement type="package" version="1.2">samtools</requirement>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
10 </requirements>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
11 <command>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
12
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
13 ## prepare bowtie2 index
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
14 #set index_path = ''
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
15 #if str($reference_genome.source) == "history":
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
16 bowtie2-build "$reference_genome.own_file" genome &amp;&amp;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
17 ln -s "$reference_genome.own_file" genome.fa &amp;&amp;
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
18 #set index_path = 'genome'
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
19 #else:
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
20 #set index_path = $reference_genome.index.fields.path
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
21 #end if
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
22
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
23 ## execute bowtie2
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
24
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
25 bowtie2
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
26
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
27 ## number of threads
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
28 -p \${GALAXY_SLOTS:-4}
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
29
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
30 ## index file path
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
31 -x $index_path
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
32
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
33 ## Fastq inputs
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
34 #if str( $library.type ) == "single":
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
35 -U "${library.input_1}"
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
36 #if str( $library.unaligned_file ) == "true":
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
37 --un $output_unaligned_reads_l
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
38 #end if
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
39 #elif str( $library.type ) == "paired":
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
40 -1 "${library.input_1}"
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
41 -2 "${library.input_2}"
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
42 #if str( $library.paired_options.paired_options_selector ) == "yes":
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
43 -I "${library.paired_options.I}"
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
44 -X "${library.paired_options.X}"
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
45 ${library.paired_options.fr_rf_ff}
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
46 ${library.paired_options.no_mixed}
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
47 ${library.paired_options.no_discordant}
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
48 ${library.paired_options.dovetail}
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
49 ${library.paired_options.no_contain}
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
50 ${library.paired_options.no_overlap}
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
51 #end if
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
52 #if str( $library.unaligned_file ) == "true":
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
53 --un-conc $output_unaligned_reads_l
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
54 #end if
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
55 #else
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
56 ## prepare collection
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
57 -1 $library.input_1.forward
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
58 -2 $library.input_1.reverse
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
59 #if str( $library.paired_options.paired_options_selector ) == "yes":
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
60 -I "${library.paired_options.I}"
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
61 -X "${library.paired_options.X}"
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
62 ${library.paired_options.fr_rf_ff}
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
63 ${library.paired_options.no_mixed}
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
64 ${library.paired_options.no_discordant}
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
65 ${library.paired_options.dovetail}
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
66 ${library.paired_options.no_contain}
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
67 ${library.paired_options.no_overlap}
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
68 #end if
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
69 #if str( $library.unaligned_file ) == "true":
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
70 --un-conc $output_unaligned_reads_l
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
71 #end if
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
72 #end if
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
73
5
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
74 ## Read group information.
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
75 @define_read_group_helpers@
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
76 #if str( $library.type ) == "single":
6
e23b0cdeeba6 planemo upload commit 5ad726dc73203a704666033cd3bf70b82575978f
devteam
parents: 5
diff changeset
77 #set $rg_auto_name = $read_group_name_default($library.input_1)
5
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
78 #elif str( $library.type ) == "paired":
6
e23b0cdeeba6 planemo upload commit 5ad726dc73203a704666033cd3bf70b82575978f
devteam
parents: 5
diff changeset
79 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
5
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
80 #else
6
e23b0cdeeba6 planemo upload commit 5ad726dc73203a704666033cd3bf70b82575978f
devteam
parents: 5
diff changeset
81 #set $rg_auto_name = $read_group_name_default($library.input_1)
5
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
82 #end if
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
83 @set_use_rg_var@
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
84 @set_read_group_vars@
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
85 #if $use_rg
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
86 $format_read_group("", $rg_id, '"', arg='--rg-id ')
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
87 $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
88 $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
89 $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
90 $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
91 $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
92 $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
93 $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
94 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
95 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
96 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
97 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
98 #end if
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
99
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
100 ## Analysis type
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
101 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
102 $analysis_type.presets
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
103 #elif str( $analysis_type.analysis_type_selector ) == "full":
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
104 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
105 --skip "${analysis_type.input_options.skip}"
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
106 --qupto "${analysis_type.input_options.qupto}"
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
107 --trim5 "${analysis_type.input_options.trim5}"
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
108 --trim3 "${analysis_type.input_options.trim3}"
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
109 ${analysis_type.input_options.qv_encoding}
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
110 ${analysis_type.input_options.solexa_quals}
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
111 ${analysis_type.input_options.int_quals}
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
112 #end if
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
113
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
114 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
115 -N "${analysis_type.alignment_options.N}"
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
116 -L "${analysis_type.alignment_options.L}"
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
117 -i "${analysis_type.alignment_options.i}"
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
118 --n-ceil "${analysis_type.alignment_options.n_ceil}"
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
119 --dpad "${analysis_type.alignment_options.dpad}"
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
120 --gbar "${analysis_type.alignment_options.gbar}"
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
121 ${analysis_type.alignment_options.ignore_quals}
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
122 ${analysis_type.alignment_options.nofw}
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
123 ${analysis_type.alignment_options.norc}
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
124 ${analysis_type.alignment_options.no_1mm_upfront}
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
125 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
126 --end-to-end
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
127 --score-min "${analysis_type.alignment_options.align_mode.score_min_ete}"
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
128 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
129 --local
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
130 --score-min "${analysis_type.alignment_options.align_mode.score_min_loc}"
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
131 #end if
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
132 #end if
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
133
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
134 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
135 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
136 --ma "${analysis_type.scoring_options.ma}"
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
137 #end if
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
138 --mp "${analysis_type.scoring_options.mp}"
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
139 --np "${analysis_type.scoring_options.np}"
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
140 --rdg "${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}"
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
141 --rfg "${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}"
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
142 #end if
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
143
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
144 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
145 -k "${analysis_type.reporting_options.k}"
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
146 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
147 -a
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
148 #end if
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
149
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
150 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
151 -D "${analysis_type.effort_options.D}"
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
152 -R "${analysis_type.effort_options.R}"
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
153 #end if
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
154
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
155 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
156 ${analysis_type.sam_options.no_unal}
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
157 ${analysis_type.sam_options.omit_sec_seq}
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
158 #end if
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
159
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
160 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
161 ${analysis_type.other_options.reorder}
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
162 ${analysis_type.other_options.non_deterministic}
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
163 --seed "${analysis_type.other_options.seed}"
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
164 #end if
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
165
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
166 #elif str( $analysis_type.analysis_type_selector ) == "cline":
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
167 ${analysis_type.cline}
4
1fc845afa3ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 32fe80982b5c59687eece667f0372002588566f8-dirty
devteam
parents: 3
diff changeset
168 #end if
1fc845afa3ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 32fe80982b5c59687eece667f0372002588566f8-dirty
devteam
parents: 3
diff changeset
169
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
170 ## output file
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
171 #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
172 | samtools view -Su - | samtools sort -o - - &gt; $output
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
173 #else
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
174 &gt; $output_sam
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
175 #end if
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
176
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
177 ## rename unaligned sequence files
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
178 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
4
1fc845afa3ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 32fe80982b5c59687eece667f0372002588566f8-dirty
devteam
parents: 3
diff changeset
179 #from os.path import splitext
1fc845afa3ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 32fe80982b5c59687eece667f0372002588566f8-dirty
devteam
parents: 3
diff changeset
180 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
1fc845afa3ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 32fe80982b5c59687eece667f0372002588566f8-dirty
devteam
parents: 3
diff changeset
181 &amp;&amp; mv "${ _unaligned_root }.1${_unaligned_ext}" "${ output_unaligned_reads_l }"
1fc845afa3ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 32fe80982b5c59687eece667f0372002588566f8-dirty
devteam
parents: 3
diff changeset
182 &amp;&amp; mv "${ _unaligned_root }.2${_unaligned_ext}" "${ output_unaligned_reads_r }"
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
183 #end if
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
184
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
185 </command>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
186 <!-- basic error handling -->
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
187 <stdio>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
188 <exit_code range="1:" level="fatal" description="Tool exception" />
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
189 </stdio>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
190
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
191 <inputs>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
192 <!-- single/paired -->
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
193 <conditional name="library">
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
194 <param name="type" type="select" label="Is this single or paired library">
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
195 <option value="single">Single-end</option>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
196 <option value="paired">Paired-end</option>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
197 <option value="paired_collection">Paired-end Dataset Collection</option>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
198 </param>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
199
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
200 <when value="single">
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
201 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
202 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
203 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
204 <when value="paired">
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
205 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
206 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
207 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
208 <conditional name="paired_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
209 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
210 <option value="no" selected="True">No</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
211 <option value="yes">Yes</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
212 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
213 <when value="yes">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
214 <param name="I" type="integer" value="0" min="0" label="Set the minimum fragment length for valid paired-end alignments" help="-I/--minins; E.g. if `-I 60` is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as `-X` is also satisfied). A 19-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-I` constraint is applied with respect to the untrimmed mates. The larger the difference between `-I` and `-X`, the slower Bowtie 2 will run. This is because larger differences bewteen `-I` and `-X` require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. Default=0"/>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
215 <param name="X" type="integer" value="500" min="0" label="Set the maximum fragment length for valid paired-end alignments" help="-X/--maxins; E.g. if `-X 100` is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-X` constraint is applied with respect to the untrimmed mates, not the trimmed mates; Default=500"/>
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
216 <param name="fr_rf_ff" type="select" display="radio" label="Select the upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand" help="--fr, --rf, or --ff; E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)">
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
217 <option value="--fr" selected="True">--fr</option>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
218 <option value="--rf">--rf</option>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
219 <option value="--ff">--ff</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
220 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
221 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
222 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
223 <param name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
224 <param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
225 <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
226 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
227 <when value="no">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
228 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
229 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
230 </conditional>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
231 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
232 <when value="paired_collection">
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
233 <param name="input_1" format="fastqsanger" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot;" />
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
234 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
235 <conditional name="paired_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
236 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
237 <option value="no" selected="True">No</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
238 <option value="yes">Yes</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
239 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
240 <when value="yes">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
241 <param name="I" type="integer" value="0" min="0" label="Set the minimum fragment length for valid paired-end alignments" help="-I/--minins; E.g. if `-I 60` is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as `-X` is also satisfied). A 19-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-I` constraint is applied with respect to the untrimmed mates. The larger the difference between `-I` and `-X`, the slower Bowtie 2 will run. This is because larger differences bewteen `-I` and `-X` require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. Default=0"/>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
242 <param name="X" type="integer" value="500" min="0" label="Set the maximum fragment length for valid paired-end alignments" help="-X/--maxins; E.g. if `-X 100` is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-X` constraint is applied with respect to the untrimmed mates, not the trimmed mates; Default=500"/>
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
243 <param name="fr_rf_ff" type="select" display="radio" label="Select the upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand" help="--fr, --rf, or --ff; E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)">
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
244 <option value="--fr" selected="True">--fr</option>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
245 <option value="--rf">--rf</option>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
246 <option value="--ff">--ff</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
247 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
248 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
249 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
250 <param name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
251 <param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
252 <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
253 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
254 <when value="no">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
255 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
256 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
257 </conditional>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
258 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
259 </conditional>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
260
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
261 <!-- reference genome -->
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
262 <conditional name="reference_genome">
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
263 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
264 <option value="indexed">Use a built-in genome index</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
265 <option value="history">Use a genome from the history and build index</option>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
266 </param>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
267 <when value="indexed">
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
268 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
269 <options from_data_table="bowtie2_indexes">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
270 <filter type="sort_by" column="2"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
271 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
272 </options>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
273 </param>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
274 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
275 <when value="history">
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
276 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
277 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
278 </conditional>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
279
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
280 <!-- read group settings -->
5
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
281 <expand macro="read_group_conditional" />
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
282 <conditional name="analysis_type">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
283 <param name="analysis_type_selector" type="select" label="Select analysis mode">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
284 <option value="simple">1: Default setting only</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
285 <option value="full">2: Full parameter list</option>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
286 </param>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
287 <when value="simple">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
288 <param name="presets" type="select" display="radio" label="Do you want to use presets?" help="Allow selecting among several preset parameter settings. Choosing between these will result in dramatic changes in runtime. See help below to understand effects of these presets.">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
289 <option value="no_presets" selected="True">No, just use defaults</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
290 <option value="--very-fast">Very fast end-to-end (--very-fast)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
291 <option value="--fast">Fast end-to-end (--fast)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
292 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
293 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
294 <option value="--very-fast-local">Very fast local (--very-fast-local)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
295 <option value="--fast-local">Fast local (--fast-local)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
296 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
297 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
298 </param>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
299 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
300 <when value="full">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
301 <conditional name="input_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
302 <param name="input_options_selector" type="select" label="Do you want to tweak input options?" help="See &quot;Input Options&quot; section of Help below for information">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
303 <option value="yes">Yes</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
304 <option value="no" selected="true">No</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
305 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
306 <when value="yes">
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
307 <param name="skip" type="integer" min="0" value="0" label="Skip (i.e. do not align) the first that many reads or pairs in the input" help="-s/--skip; default=0"/>
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
308 <param name="qupto" type="integer" min="1" value="100000000" label="Align the first that many reads or read pairs from the input (after the -s/--skip reads or pairs have been skipped), then stop" help="-u/--qupto; for default behavior (no limit) leave this value very large"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
309 <param name="trim5" type="integer" min="0" value="0" label="Trim that many bases from 5' (left) end of each read before alignment" help="-5/--trim5; default=0"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
310 <param name="trim3" type="integer" min="0" value="0" label="Trim that many bases from 3' (right) end of each read before alignment" help="-3/--trim3; default=0"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
311 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
312 <option value="--phred33" selected="True">Input qualities are ASCII chars equal to the Phred quality plus 33. This is also called the "Phred+33" encoding, which is used by the very latest Illumina pipelines (--phred33)</option>
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
313 <option value="--phred64">Input qualities are ASCII chars equal to the Phred quality plus 64. This is also called the "Phred+64" encoding (--phred64)</option>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
314 </param>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
315 <param name="solexa_quals" type="boolean" truevalue="--solexa-quals" falsevalue="" checked="False" label="Convert input qualities from Solexa (which can be negative) to Phred (which can't). This scheme was used in older Illumina GA Pipeline versions (prior to 1.3)" help="--solexa-quals; default=False"/>
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
316 <param name="int_quals" type="boolean" truevalue="--int-quals" falsevalue="" checked="False" label="Quality values are represented in the read input file as space-separated ASCII integers, e.g., 40 40 30 40..., rather than ASCII characters, e.g., II?I.... Integers are treated as being on the Phred quality scale unless --solexa-quals is also specified" help="--int-quals; default=False"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
317 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
318 <when value="no">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
319 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
320 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
321 </conditional>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
322 <conditional name="alignment_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
323 <param name="alignment_options_selector" type="select" label="Do you want to tweak alignment options?" help="See &quot;Alignment Options&quot; section of Help below for information">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
324 <option value="yes">Yes</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
325 <option value="no" selected="true">No</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
326 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
327 <when value="yes">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
328 <param name="N" type="integer" min="0" max="1" value="0" label="Set the number of mismatches to be allowed in a seed alignment during multiseed alignment (see `Multiseed alignment` section of help below)" help="-N; Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity; default=0"/>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
329 <param name="L" type="integer" min="0" max="32" value="22" label="Sets the length of the seed substrings to align during multiseed alignment (see `Multiseed alignment` section of help below)" help="-L; Smaller values make alignment slower but more sensitive. Default=22"/>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
330 <param name="i" type="text" value="S,1,1.15" label="Set a function governing the interval between seed substrings to use during multiseed alignment (see `Multiseed alignment` section of help below). Also see description of this option below in the help section" help="-i; Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. If the function returns a result less than 1, it is rounded up to 1. Default=`S,1,1.15`"/>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
331 <param name="n_ceil" type="text" value="L,0,0.15" label="Set a function governing the maximum number of ambiguous characters (usually `N`s and/or `.`s) allowed in a read as a function of read length" help="--n-ceil; For instance, specifying `L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, where x is the read length. Reads exceeding this ceiling are filtered out. Default=`L,0,0.15`"/>
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
332 <param name="dpad" type="integer" min="0" value="15" label="Pad dynamic programming problems by that many columns on either side to allow gaps" help="--dpad; default=15"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
333 <param name="gbar" type="integer" min="0" value="4" label="Disallow gaps within that many positions of the beginning or end of the read" help="--gbar; default=4"/>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
334 <param name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" selected="False" label="When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value" help="--ignore-quals; input is treated as though all quality values are high; default=False"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
335 <param name="nofw" type="boolean" truevalue="--nofw" falsevalue="" selected="False" label="Do not attempt to align unpaired reads to the forward (Watson) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
336 <param name="norc" type="boolean" truevalue="--norc" falsevalue="" selected="False" label="Do not attempt to align unpaired reads to the reverse (Crick) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
337 <param name="no_1mm_upfront" type="boolean" truevalue="--no-1mm-upfront" falsevalue="" selected="False" label="Prevent searching for 1-mismatch end-to-end alignments before using the multiseed heuristic (see `Multiseed alignment` section of help below)" help="--no-1mm-upfront; By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch end-to-end alignment for the read *before* trying the multiseed heuristic. Such alignments can be found very quickly, and many short read alignments have exact or near-exact end-to-end alignments. However, this can lead to unexpected alignments when the user also sets options governing the multiseed heuristic, like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal to the length of the read, the user will be surprised to find 1-mismatch alignments reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end alignments before using the multiseed heuristic, which leads to the expected behavior when combined with options such as `-L` and `-N`. This comes at the expense of speed; Default=False"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
338 <conditional name="align_mode">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
339 <param name="align_mode_selector" type="select" display="radio" label="Select between `--local` and `--end-to-end` alignment modes" help="--local and --end-to-end; see help below for detailed explanation; default=--end-to-end">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
340 <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
341 <option value="local">Local (--local)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
342 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
343 <when value="end-to-end">
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
344 <param name="score_min_ete" type="text" value="L,-0.6,-0.6" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
345 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
346 <when value="local">
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
347 <param name="score_min_loc" type="text" value="G,20,8" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
348 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
349 </conditional>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
350 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
351 <when value="no">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
352 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
353 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
354 </conditional>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
355 <conditional name="scoring_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
356 <param name="scoring_options_selector" type="select" label="Do you want to tweak scoring options?" help="See &quot;Scoring Options&quot; section of Help below for information">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
357 <option value="yes">Yes</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
358 <option value="no" selected="true">No</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
359 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
360 <when value="yes">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
361 <param name="ma" type="integer" value="2" label="Set the match bonus" help="--ma; In `--local` mode match bonus is added to the alignment score for each position where a read character aligns to a reference character and the characters match. Not used in `--end-to-end` mode; Default=2"/>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
362 <param name="mp" type="text" value="6,2" label="Set the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers" help="--mp; A number less than or equal to `MX` and greater than or equal to `MN` is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`. Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` where Q is the Phred quality value; Default=6,2"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
363 <param name="np" type="integer" value="1" label="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as `N`" help="--np; Default=1"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
364 <param name="rdg_read_open" type="integer" value="5" label="Set the read gap opening penalty" help="--rdg; this is the first component of --rdg flag - opening penalty; Default=5"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
365 <param name="rdg_read_extend" type="integer" value="3" label="Set the read gap extension penalty" help="--rdg; this is the second component of --rdg flag - extension penalty; Default=3"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
366 <param name="rfg_ref_open" type="integer" value="5" label="Set the reference gap opening penalty" help="--rfg; this is the first component of --rfg flag - opening penalty; Default=5"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
367 <param name="rfg_ref_extend" type="integer" value="3" label="Set the reference gap extension penalty" help="--rfg; this is the second component of --rfg flag - extension penalty; Default=3"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
368 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
369 <when value="no">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
370 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
371 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
372 </conditional>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
373 <conditional name="reporting_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
374 <param name="reporting_options_selector" type="select" label="Do you want to use -a or -k options" help="Make sure you understand implications of setting -k and -a. See &quot;Reporting Options&quot; section of Help below for information on -k and -a options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
375 <option value="no" selected="true">No, do not set</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
376 <option value="k">Set -k option and enter -k value</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
377 <option value="a">Set -a option</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
378 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
379 <when value="no">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
380 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
381 </when>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
382 <when value="k">
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
383 <param name="k" type="integer" min="1" value="1" label="Searches for at most that many distinct, valid alignments for each read" help="-k; see detailed description of this option in the help section below. Note: Bowtie 2 is not designed with large values for `-k` in mind, and when aligning reads to long, repetitive genomes large `-k` can be very, very slow"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
384 </when>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
385 <when value="a">
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
386 <!-- do nothing here; set -a flag on the command line-->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
387 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
388 </conditional>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
389 <conditional name="effort_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
390 <param name="effort_options_selector" type="select" label="Do you want to tweak effort options?" help="See &quot;Effort Options&quot; section of Help below for information">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
391 <option value="yes">Yes</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
392 <option value="no" selected="true">No</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
393 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
394 <when value="yes">
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
395 <param name="D" type="integer" value="15" min="0" label="Attempt that many consecutive seed extension attempts to `fail` before Bowtie 2 moves on, using the alignments found so far" help="-D; A seed extension `fails` if it does not yield a new best or a new second-best alignment. This limit is automatically adjusted up when -k or -a are specified. Default=15"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
396 <param name="R" type="integer" value="2" min="0" label="Set the maximum number of times Bowtie 2 will `re-seed` reads with repetitive seeds" help="When `re-seeding`, Bowtie 2 simply chooses a new set of reads (same length, same number of mismatches allowed) at different offsets and searches for more alignments. A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than 300. Default=2"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
397 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
398 <when value="no">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
399 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
400 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
401 </conditional>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
402
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
403 <conditional name="sam_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
404 <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See &quot;Output Options&quot; section of Help below for information">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
405 <option value="yes">Yes</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
406 <option value="no" selected="true">No</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
407 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
408 <when value="yes">
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
409 <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
410 <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
411 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
412 <when value="no">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
413 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
414 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
415 </conditional>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
416 <conditional name="other_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
417 <param name="other_options_selector" type="select" label="Do you want to tweak Other Options?" help="See &quot;Other Options&quot; section of Help below for information">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
418 <option value="yes">Yes</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
419 <option value="no" selected="true">No</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
420 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
421 <when value="yes">
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
422 <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" label="Guarantee that output SAM records are printed in an order corresponding to the order of the reads in the original input file" help="--reorder; Default=False"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
423 <param name="seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="--seed; Default=0"/>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
424 <param name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="--non-deterministic; see Help below for explanation of this option; default=False"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
425 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
426 <when value="no">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
427 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
428 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
429 </conditional>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
430 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
431 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
432 </conditional>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
433 </inputs>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
434
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
435 <!-- define outputs -->
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
436
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
437 <outputs>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
438
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
439 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
440 <filter>library['unaligned_file'] is True</filter>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
441 <actions>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
442 <conditional name="library.type">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
443 <when value="single">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
444 <action type="format">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
445 <option type="from_param" name="library.input_1" param_attribute="ext" />
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
446 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
447 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
448 <when value="paired">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
449 <action type="format">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
450 <option type="from_param" name="library.input_1" param_attribute="ext" />
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
451 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
452 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
453 <when value="paired_collection">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
454 <action type="format">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
455 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
456 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
457 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
458 </conditional>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
459 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
460 </data>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
461 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
462 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
463 <actions>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
464 <conditional name="library.type">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
465 <when value="paired">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
466 <action type="format">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
467 <option type="from_param" name="library.input_2" param_attribute="ext" />
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
468 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
469 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
470 <when value="paired_collection">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
471 <action type="format">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
472 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
473 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
474 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
475 </conditional>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
476 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
477 </data>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
478
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
479 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
480 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
481 <actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
482 <conditional name="reference_genome.source">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
483 <when value="indexed">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
484 <action type="metadata" name="dbkey">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
485 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
486 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
487 <filter type="param_value" ref="reference_genome.index" column="0"/>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
488 </option>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
489 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
490 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
491 <when value="history">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
492 <action type="metadata" name="dbkey">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
493 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
494 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
495 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
496 </conditional>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
497 </actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
498 </data>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
499
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
500 <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
501 <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
502 <actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
503 <conditional name="reference_genome.source">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
504 <when value="indexed">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
505 <action type="metadata" name="dbkey">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
506 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
507 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
508 <filter type="param_value" ref="reference_genome.index" column="0"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
509 </option>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
510 </action>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
511 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
512 <when value="history">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
513 <action type="metadata" name="dbkey">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
514 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
515 </action>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
516 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
517 </conditional>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
518 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
519 </data>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
520
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
521 </outputs>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
522
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
523 <tests>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
524 <test>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
525 <!-- basic test on single paired default run -->
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
526 <param name="type" value="paired"/>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
527 <param name="selection" value="no"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
528 <param name="paired_options_selector" value="no"/>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
529 <param name="unaligned_file" value="false"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
530 <param name="analysis_type_selector" value="simple"/>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
531 <param name="source" value="history" />
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
532 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
533 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
534 <param name="own_file" value="bowtie2-ref.fasta" />
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
535 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
536 </test>
5
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
537 <test>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
538 <!-- basic test on single paired default run -->
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
539 <param name="type" value="paired"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
540 <param name="selection" value="no"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
541 <param name="paired_options_selector" value="no"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
542 <param name="unaligned_file" value="false"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
543 <param name="analysis_type_selector" value="simple"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
544 <param name="rg_selector" value="set"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
545 <param name="ID" value="rg1"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
546 <param name="PL" value="CAPILLARY"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
547 <param name="source" value="history" />
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
548 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
549 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
550 <param name="own_file" value="bowtie2-ref.fasta" />
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
551 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
552 </test>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
553 </tests>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
554
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
555 <help>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
556
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
557 **Bowtie2 Overview**
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
558
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
559 Bowtie2_ is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 supports gapped, local, and paired-end alignment modes. Galaxy wrapper for Bowtie 2 outputs alignments in `BAM format`_, enabling interoperation with a large number of other tools available at this site.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
560 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
561
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
562 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
563 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
564 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
565
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
566 -----
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
567
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
568 **Selecting reference genomes for Bowtie2**
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
569
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
570 Galaxy wrapper for Bowtie2 allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
571
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
572 1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bowtie2-build utility and are ready to be mapped against.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
573 2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome from this dropdown will cause Galaxy to first transparently index it using bowtie2-build command, and then run mapping with bowtie2.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
574
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
575 If your genome of interest is not listed here you have two choices:
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
576
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
577 1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
578 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
579
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
580 ------
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
581
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
582 .. class:: infomark
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
583
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
584 **Bowtie2 options**
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
585
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
586 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
587
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
588 -----
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
589
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
590 **Inputs**
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
591
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
592 Bowtie 2 accepts files in Sanger FASTQ format (single or pair-end). Use the FASTQ Groomer to prepare your files.
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
593
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
594 ------
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
595
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
596 **Input options**::
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
597
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
598 -s/--skip &lt;int&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
599 Skip (i.e. do not align) the first `&lt;int&gt;` reads or pairs in the input.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
600
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
601 -u/--qupto &lt;int&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
602 Align the first `&lt;int&gt;` reads or read pairs from the input (after the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
603 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
604
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
605 -5/--trim5 &lt;int&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
606 Trim `&lt;int&gt;` bases from 5' (left) end of each read before alignment (default: 0).
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
607
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
608 -3/--trim3 &lt;int&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
609 Trim `&lt;int&gt;` bases from 3' (right) end of each read before alignment (default: 0).
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
610
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
611 --phred33
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
612 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
613 also called the "Phred+33" encoding, which is used by the very latest Illumina
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
614 pipelines.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
615
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
616 --phred64
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
617 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
618 also called the "Phred+64" encoding.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
619
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
620 --solexa-quals
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
621 Convert input qualities from Solexa Phred quality (which can be negative) to
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
622 Phred Phred quality (which can't). This scheme was used in older Illumina GA
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
623 Pipeline versions (prior to 1.3). Default: off.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
624
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
625 --int-quals
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
626 Quality values are represented in the read input file as space-separated ASCII integers, e.g., `40 40 30 40`..., rather than ASCII characters, e.g., `II?I`....
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
627 Integers are treated as being on the Phred quality scale unless
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
628 `--solexa-quals` is also specified. Default: off.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
629
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
630 ------
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
631
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
632 **Presets in `--end-to-end` mode**::
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
633
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
634 --very-fast
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
635 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
636
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
637 --fast
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
638 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
639
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
640 --sensitive
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
641 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
642
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
643 --very-sensitive
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
644 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
645
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
646 ------
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
647
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
648 **Presets options in `--local` mode**::
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
649
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
650 --very-fast-local
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
651 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00`
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
652
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
653 --fast-local
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
654 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75`
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
655
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
656 --sensitive-local
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
657 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
658
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
659 --very-sensitive-local
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
660 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
661
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
662 ------
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
663
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
664 **Alignment options**::
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
665
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
666 -N &lt;int&gt;
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
667 Sets the number of mismatches to allowed in a seed alignment during multiseed
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
668 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
669 (often much slower) but increases sensitivity. Default: 0.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
670
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
671 -L &lt;int&gt;
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
672 Sets the length of the seed substrings to align during multiseed alignment.
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
673 Smaller values make alignment slower but more sensitive. Default: the
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
674 `--sensitive` preset is used by default, which sets `-L` to 22 in
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
675 `--end-to-end` mode and to 20 in `--local` mode.
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
676
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
677 -i &lt;func&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
678 Sets a function governing the interval between seed substrings to use during
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
679 multiseed alignment. For instance, if the read has 30 characers, and seed
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
680 length is 10, and the seed interval is 6, the seeds extracted will be:
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
681
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
682 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
683 Seed 1 fw: TAGCTACGCT
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
684 Seed 1 rc: AGCGTAGCTA
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
685 Seed 2 fw: CGCTCTACGC
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
686 Seed 2 rc: GCGTAGAGCG
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
687 Seed 3 fw: ACGCTATCAT
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
688 Seed 3 rc: ATGATAGCGT
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
689 Seed 4 fw: TCATGCATAA
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
690 Seed 4 rc: TTATGCATGA
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
691
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
692 Since it's best to use longer intervals for longer reads, this parameter sets
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
693 the interval as a function of the read length, rather than a single
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
694 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
695 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length.
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
696 If the function returns a result less than
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
697 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
698 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
699 in `--local` mode.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
700
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
701 --n-ceil &lt;func&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
702 Sets a function governing the maximum number of ambiguous characters (usually
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
703 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
704 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
705 where x is the read length. Reads exceeding this ceiling are filtered out.
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
706 Default: `L,0,0.15`.
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
707
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
708 --dpad &lt;int&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
709 "Pads" dynamic programming problems by `&lt;int&gt;` columns on either side to allow
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
710 gaps. Default: 15.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
711
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
712 --gbar &lt;int&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
713 Disallow gaps within `&lt;int&gt;` positions of the beginning or end of the read.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
714 Default: 4.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
715
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
716 --ignore-quals
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
717 When calculating a mismatch penalty, always consider the quality value at the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
718 mismatched position to be the highest possible, regardless of the actual value.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
719 I.e. input is treated as though all quality values are high. This is also the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
720 default behavior when the input doesn't specify quality values (e.g. in `-f`,
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
721 `-r`, or `-c` modes).
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
722
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
723 --nofw/--norc
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
724 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
725 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
726 not attempt to align unpaired reads against the reverse-complement (Crick)
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
727 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
728 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
729 paired-end configurations corresponding to fragments from the reverse-complement
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
730 (Crick) strand. Default: both strands enabled.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
731
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
732 --no-1mm-upfront
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
733 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
734 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
735 alignments can be found very quickly, and many short read alignments have exact or
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
736 near-exact end-to-end alignments. However, this can lead to unexpected
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
737 alignments when the user also sets options governing the multiseed heuristic,
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
738 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
739 to the length of the read, the user will be surprised to find 1-mismatch alignments
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
740 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
741 alignments before using the multiseed heuristic, which leads to the expected
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
742 behavior when combined with options such as `-L` and `-N`. This comes at the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
743 expense of speed.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
744
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
745 --end-to-end
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
746 In this mode, Bowtie 2 requires that the entire read align from one end to the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
747 other, without any trimming (or "soft clipping") of characters from either end.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
748 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
749 are less than or equal to 0, and the greatest possible alignment score is 0.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
750 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
751
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
752 --local
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
753 In this mode, Bowtie 2 does not require that the entire read align from one end
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
754 to the other. Rather, some characters may be omitted ("soft clipped") from the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
755 ends in order to achieve the greatest possible alignment score. The match bonus
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
756 `--ma` is used in this mode, and the best possible alignment score is equal to
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
757 the match bonus (`--ma`) times the length of the read. Specifying `--local`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
758 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
759 the local version of the preset (`--very-fast-local`). This is mutually
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
760 exclusive with `--end-to-end`. `--end-to-end` is the default mode.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
761
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
762 -----
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
763
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
764 **Scoring options**::
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
765
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
766 --ma &lt;int&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
767 Sets the match bonus. In `--local` mode `&lt;int&gt;` is added to the alignment
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
768 score for each position where a read character aligns to a reference character
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
769 and the characters match. Not used in `--end-to-end` mode. Default: 2.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
770
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
771 --mp MX,MN
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
772 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
773 number less than or equal to `MX` and greater than or equal to `MN` is
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
774 subtracted from the alignment score for each position where a read character
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
775 aligns to a reference character, the characters do not match, and neither is an
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
776 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
777 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
778 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
779
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
780 --np &lt;int&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
781 Sets penalty for positions where the read, reference, or both, contain an
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
782 ambiguous character such as `N`. Default: 1.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
783
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
784 --rdg &lt;int1&gt;,&lt;int2&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
785 Sets the read gap open (`&lt;int1&gt;`) and extend (`&lt;int2&gt;`) penalties. A read gap of
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
786 length N gets a penalty of `&lt;int1&gt;` + N * `&lt;int2&gt;`. Default: 5, 3.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
787
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
788 --rfg &lt;int1&gt;,&lt;int2&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
789 Sets the reference gap open (`&lt;int1&gt;`) and extend (`&lt;int2&gt;`) penalties. A
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
790 reference gap of length N gets a penalty of `&lt;int1&gt;` + N * `&lt;int2&gt;`. Default:
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
791 5, 3.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
792
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
793 --score-min &lt;func&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
794 Sets a function governing the minimum alignment score needed for an alignment to
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
795 be considered "valid" (i.e. good enough to report). This is a function of read
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
796 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
797 to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
798 the default in `--local` mode is `G,20,8`.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
799
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
800 -----
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
801
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
802 **Reporting options**::
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
803
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
804 -k &lt;int&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
805 By default, `bowtie2` searches for distinct, valid alignments for each read.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
806 When it finds a valid alignment, it continues looking for alignments that are
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
807 nearly as good or better. The best alignment found is reported (randomly
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
808 selected from among best if tied). Information about the best alignments is
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
809 used to estimate mapping quality and to set SAM optional fields, such as
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
810 `AS:i` and `XS:i`.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
811
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
812 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
813 searches for at most `&lt;int&gt;` distinct, valid alignments for each read. The
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
814 search terminates when it can't find more distinct valid alignments, or when it
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
815 finds `&lt;int&gt;`, whichever happens first. All alignments found are reported in
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
816 descending order by alignment score. The alignment score for a paired-end
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
817 alignment equals the sum of the alignment scores of the individual mates. Each
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
818 reported read or pair alignment beyond the first has the SAM 'secondary' bit
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
819 (which equals 256) set in its FLAGS field. For reads that have more than
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
820 `&lt;int&gt;` distinct, valid alignments, `bowtie2` does not guarantee that the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
821 `&lt;int&gt;` alignments reported are the best possible in terms of alignment score.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
822 `-k` is mutually exclusive with `-a`.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
823
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
824 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
825 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
826
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
827 -a
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
828 Like `-k` but with no upper limit on number of alignments to search for. `-a`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
829 is mutually exclusive with `-k`.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
830
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
831 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
832 aligning reads to long, repetitive genomes this mode can be very, very slow.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
833
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
834 -----
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
835
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
836 **Effort options**::
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
837
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
838 -D &lt;int&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
839 Up to `&lt;int&gt;` consecutive seed extension attempts can "fail" before Bowtie 2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
840 moves on, using the alignments found so far. A seed extension "fails" if it
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
841 does not yield a new best or a new second-best alignment. This limit is
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
842 automatically adjusted up when -k or -a are specified. Default: 15.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
843
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
844 -R &lt;int&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
845 `&lt;int&gt;` is the maximum number of times Bowtie 2 will "re-seed" reads with
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
846 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
847 (same length, same number of mismatches allowed) at different offsets and
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
848 searches for more alignments. A read is considered to have repetitive seeds if
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
849 the total number of seed hits divided by the number of seeds that aligned at
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
850 least once is greater than 300. Default: 2.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
851
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
852 -----
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
853
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
854 **Paired-end options**::
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
855
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
856 -I/--minins &lt;int&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
857 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
858 specified and a paired-end alignment consists of two 20-bp alignments in the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
859 appropriate orientation with a 20-bp gap between them, that alignment is
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
860 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
861 be valid in that case. If trimming options `-3` or `-5` are also used, the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
862 `-I` constraint is applied with respect to the untrimmed mates.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
863
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
864 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
865 run. This is because larger differences bewteen `-I` and `-X` require that
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
866 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
867 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
868 efficient.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
869
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
870 Default: 0 (essentially imposing no minimum)
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
871
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
872 -X/--maxins &lt;int&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
873 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
874 is specified and a paired-end alignment consists of two 20-bp alignments in the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
875 proper orientation with a 60-bp gap between them, that alignment is considered
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
876 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
877 that case. If trimming options `-3` or `-5` are also used, the `-X`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
878 constraint is applied with respect to the untrimmed mates, not the trimmed
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
879 mates.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
880
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
881 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
882 run. This is because larger differences bewteen `-I` and `-X` require that
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
883 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
884 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
885 efficient.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
886
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
887 Default: 500.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
888
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
889 --fr/--rf/--ff
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
890 The upstream/downstream mate orientations for a valid paired-end alignment
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
891 against the forward reference strand. E.g., if `--fr` is specified and there is
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
892 a candidate paired-end alignment where mate 1 appears upstream of the reverse
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
893 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
894 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
895 complement of mate 1 and all other constraints are met, that too is valid.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
896 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
897 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
898 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
899 for Illumina's Paired-end Sequencing Assay).
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
900
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
901 --no-mixed
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
902 By default, when `bowtie2` cannot find a concordant or discordant alignment for
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
903 a pair, it then tries to find alignments for the individual mates. This option
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
904 disables that behavior.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
905
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
906 --no-discordant
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
907 By default, `bowtie2` looks for discordant alignments if it cannot find any
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
908 concordant alignments. A discordant alignment is an alignment where both mates
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
909 align uniquely, but that does not satisfy the paired-end constraints
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
910 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
911
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
912 --dovetail
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
913 If the mates "dovetail", that is if one mate alignment extends past the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
914 beginning of the other such that the wrong mate begins upstream, consider that
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
915 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
916
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
917 --no-contain
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
918 If one mate alignment contains the other, consider that to be non-concordant.
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
919 Default: a mate can contain the other in a concordant alignment.
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
920
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
921 --no-overlap
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
922 If one mate alignment overlaps the other at all, consider that to be
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
923 non-concordant. Default: mates can overlap in a concordant alignment.
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
924
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
925 ------
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
926
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
927 **SAM options**::
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
928
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
929 --rg-id &lt;text&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
930 Set the read group ID to `&lt;text&gt;`. This causes the SAM `@RG` header line to be
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
931 printed, with `&lt;text&gt;` as the value associated with the `ID:` tag. It also
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
932 causes the `RG:Z:` extra field to be attached to each SAM output record, with
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
933 value set to `&lt;text&gt;`.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
934
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
935 --rg &lt;text&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
936 Add `&lt;text&gt;` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
937 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
938 must also be specified. This is because the `ID` tag is required by the SAM
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
939 Specification. Specify `--rg` multiple times to set multiple fields. See the
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
940 SAM Specification for details about what fields are legal.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
941
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
942 --omit-sec-seq
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
943 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
944 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
945 in those fields instead.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
946
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
947 -----
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
948
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
949 **Other options**::
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
950
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
951 --reorder
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
952 Guarantees that output SAM records are printed in an order corresponding to the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
953 order of the reads in the original input file, even when `-p` is set greater
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
954 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
955 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
956 not specified. Has no effect if `-p` is set to 1, since output order will
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
957 naturally correspond to input order in that case.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
958
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
959 --seed &lt;int&gt;
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
960 Use `&lt;int&gt;` as the seed for pseudo-random number generator. Default: 0.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
961
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
962 --non-deterministic
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
963 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
964 seeds the generator with a number derived from (a) the read name, (b) the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
965 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
966 option. This means that if two reads are identical (same name, same
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
967 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
968 for both, even if there was ambiguity. When `--non-deterministic` is specified,
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
969 Bowtie 2 re-initializes its pseudo-random generator for each read using the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
970 current time. This means that Bowtie 2 will not necessarily report the same
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
971 alignment for two identical reads. This is counter-intuitive for some users,
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
972 but might be more appropriate in situations where the input consists of many
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
973 identical reads.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
974
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
975 </help>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
976 <citations>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
977 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
978 <citation type="doi">10.1038/nmeth.1923</citation>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
979 </citations>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
980 </tool>