Mercurial > repos > devteam > bowtie2

annotate bowtie2_wrapper.xml @ 20:dc1639b66f12 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 1912a560c3ad87117f18570fcf3ba4af4f924340
author iuc
date Tue, 23 Jan 2018 12:20:20 -0500
parents 97d1923c8c4b
children 3ba8d4563129
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
20
dc1639b66f12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 1912a560c3ad87117f18570fcf3ba4af4f924340
iuc
parents: 19
diff changeset
1 <tool id="bowtie2" name="Bowtie2" version="2.3.4.1" profile="17.01">
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>
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
4 <import>bowtie2_macros.xml</import>
5
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>
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
6 <requirements>
19
97d1923c8c4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a579dc125a63383d0a5f826cf5975c0035e8c35a
iuc
parents: 18
diff changeset
7 <requirement type="package" version="2.3.4">bowtie2</requirement>
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
8 <requirement type="package" version="1.6">samtools</requirement>
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
9 </requirements>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
10 <version_command>bowtie2 --version</version_command>
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
12 ## prepare bowtie2 index
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
13 #set index_path = ''
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
14 #if str($reference_genome.source) == "history":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
15 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome &&
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
16 ln -s -f '$reference_genome.own_file' genome.fa &&
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
17 #set index_path = 'genome'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
18 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
19 #set index_path = $reference_genome.index.fields.path
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
20 #end if
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
21
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
22 ## Link in the input files, so bowtie2 can tell their type
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
23
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
24 #set compressed="False"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
25 #set reads_are_fastq = True
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
26 #if str($library.type) == 'paired':
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
27 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
28 #set read1 = "input_f.fastq.gz"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
29 #set compressed = "GZ"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
30 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
31 #set read1 = "input_f.fastq.bz2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
32 #set compressed = "BZ2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
33 #else if $library.input_1.is_of_type('fasta'):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
34 #set reads_are_fastq = False
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
35 #set read1 = "input_f.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
36 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
37 #set read1 = "input_f.fastq"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
38 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
39 ln -f -s '${library.input_1}' ${read1} &&
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
40
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
41 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
42 #set read2 = "input_r.fastq.gz"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
43 #set compressed = "GZ"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
44 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
45 #set read2 = "input_r.fastq.bz2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
46 #set compressed = "BZ2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
47 #else if $library.input_2.is_of_type('fasta'):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
48 #set read2 = "input_r.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
49 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
50 #set read2 = "input_r.fastq"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
51 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
52 ln -f -s '${library.input_2}' ${read2} &&
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
53 #else if str($library.type) == 'paired_collection':
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
54 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
55 #set read1 = "input_f.fastq.gz"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
56 #set compressed = "GZ"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
57 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
58 #set read1 = "input_f.fastq.bz2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
59 #set compressed = "BZ2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
60 #else if $library.input_1.forward.is_of_type('fasta'):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
61 #set reads_are_fastq = False
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
62 #set read1 = "input_f.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
63 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
64 #set read1 = "input_f.fastq"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
65 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
66 ln -s '${library.input_1.forward}' ${read1} &&
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
67
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
68 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
69 #set read2 = "input_r.fastq.gz"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
70 #set compressed = "GZ"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
71 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
72 #set read2 = "input_r.fastq.bz2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
73 #set compressed = "BZ2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
74 #else if $library.input_1.reverse.is_of_type("fasta"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
75 #set read2 = "input_r.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
76 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
77 #set read2 = "input_r.fastq"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
78 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
79 ln -s '${library.input_1.reverse}' ${read2} &&
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
80
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
81 #else if str($library.type) == 'paired_interleaved':
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
82 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
83 #set read1 = "input_il.fastq.gz"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
84 #set compressed = "GZ"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
85 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
86 #set read1 = "input_il.fastq.bz2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
87 #set compressed = "BZ2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
88 #else if $library.input_1.is_of_type("fasta"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
89 #set reads_are_fastq = False
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
90 #set read1 = "input_il.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
91 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
92 #set read1 = "input_il.fastq"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
93 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
94 ln -s '${library.input_1}' ${read1} &&
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
95 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
96 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
97 #set read1 = "input_f.fastq.gz"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
98 #set compressed = "GZ"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
99 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
100 #set read1 = "input_f.fastq.bz2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
101 #set compressed = "BZ2"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
102 #else if $library.input_1.is_of_type("fasta"):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
103 #set reads_are_fastq = False
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
104 #set read1 = "input_f.fasta"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
105 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
106 #set read1 = "input_f.fastq"
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
107 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
108 ln -s '${library.input_1}' ${read1} &&
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
109 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
110
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
111 ## execute bowtie2
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
112
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
113 bowtie2
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
114
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
115 ## number of threads
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
116 -p \${GALAXY_SLOTS:-4}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
117
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
118 ## index file path
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
119 -x '$index_path'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
120
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
121 ## Input reads are fasta?
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
122 #if not reads_are_fastq:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
123 -f
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
124 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
125
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
126 ## Input reads
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
127 #if str( $library.type ) == "single":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
128 -U '${read1}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
129 #if str( $library.unaligned_file ) == "true":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
130 #if $compressed == "GZ":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
131 --un-gz '${output_unaligned_reads_l}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
132 #else if $compressed == "BZ2":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
133 --un-bz2 '${output_unaligned_reads_l}'
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
134 #else:
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
135 --un '${output_unaligned_reads_l}'
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
136 #end if
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
137 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
138 #if str( $library.aligned_file ) == "true":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
139 #if $compressed == "GZ":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
140 --al-gz '${output_aligned_reads_l}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
141 #else if $compressed == "BZ2":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
142 --al-bz2 '${output_aligned_reads_l}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
143 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
144 --al '${output_aligned_reads_l}'
16
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
145 #end if
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
146 #end if
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
147
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
148 #elif str( $library.type ) == "paired_interleaved":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
149 --interleaved '${read1}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
150 #if str( $library.unaligned_file ) == "true":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
151 #if $compressed == "GZ":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
152 --un-gz '${output_unaligned_reads_l}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
153 #else if $compressed == "BZ2":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
154 --un-bz2 '${output_unaligned_reads_l}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
155 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
156 --un '${output_unaligned_reads_l}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
157 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
158 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
159 #if str( $library.aligned_file ) == "true":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
160 #if $compressed == "GZ":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
161 --al-gz '${output_aligned_reads_l}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
162 #else if $compressed == "BZ2":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
163 --al-bz2 '${output_aligned_reads_l}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
164 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
165 --al '${output_aligned_reads_l}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
166 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
167 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
168 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
169 -1 '${read1}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
170 -2 '${read2}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
171 #if str( $library.unaligned_file ) == "true":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
172 #if $compressed == "GZ":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
173 --un-conc-gz '${output_unaligned_reads_l}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
174 #else if $compressed == "BZ2":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
175 --un-conc-bz2 '${output_unaligned_reads_l}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
176 #else:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
177 --un-conc '${output_unaligned_reads_l}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
178 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
179 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
180 #if str( $library.aligned_file ) == "true":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
181 #if $compressed == "GZ":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
182 --al-conc-gz '${output_aligned_reads_l}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
183 #else if $compressed == "BZ2":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
184 --al-conc-bz2 '${output_aligned_reads_l}'
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
185 #else:
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
186 --al-conc '${output_aligned_reads_l}'
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
187 #end if
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
188 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
189 #if str( $library.paired_options.paired_options_selector ) == "yes":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
190 -I ${library.paired_options.I}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
191 -X ${library.paired_options.X}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
192 ${library.paired_options.fr_rf_ff}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
193 ${library.paired_options.no_mixed}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
194 ${library.paired_options.no_discordant}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
195 ${library.paired_options.dovetail}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
196 ${library.paired_options.no_contain}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
197 ${library.paired_options.no_overlap}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
198 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
199 #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
200
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
201 ## Read group information.
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
202 @define_read_group_helpers@
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
203 #if str( $library.type ) == "single":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
204 #set $rg_auto_name = $read_group_name_default($library.input_1)
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
205 #elif str( $library.type ) == "paired":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
206 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
207 #else
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
208 #set $rg_auto_name = $read_group_name_default($library.input_1)
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
209 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
210 @set_use_rg_var@
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
211 @set_read_group_vars@
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
212 #if $use_rg
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
213 $format_read_group("", $rg_id, '"', arg='--rg-id ')
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
214 $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
215 $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
216 $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
217 $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
218 $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
219 $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
220 $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
221 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
222 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
223 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
224 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
225 #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
226
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
227 ## Analysis type
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
228 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
229 $analysis_type.presets
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
230 #elif str( $analysis_type.analysis_type_selector ) == "full":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
231 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
232 --skip ${analysis_type.input_options.skip}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
233 --qupto ${analysis_type.input_options.qupto}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
234 --trim5 ${analysis_type.input_options.trim5}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
235 --trim3 ${analysis_type.input_options.trim3}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
236 ${analysis_type.input_options.qv_encoding}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
237 ${analysis_type.input_options.solexa_quals}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
238 ${analysis_type.input_options.int_quals}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
239 #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
240
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
241 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
242 -N ${analysis_type.alignment_options.N}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
243 -L ${analysis_type.alignment_options.L}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
244 -i '${analysis_type.alignment_options.i}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
245 --n-ceil '${analysis_type.alignment_options.n_ceil}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
246 --dpad ${analysis_type.alignment_options.dpad}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
247 --gbar ${analysis_type.alignment_options.gbar}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
248 ${analysis_type.alignment_options.ignore_quals}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
249 ${analysis_type.alignment_options.nofw}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
250 ${analysis_type.alignment_options.norc}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
251 ${analysis_type.alignment_options.no_1mm_upfront}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
252 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
253 --end-to-end
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
254 --score-min '${analysis_type.alignment_options.align_mode.score_min_ete}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
255 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
256 --local
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
257 --score-min '${analysis_type.alignment_options.align_mode.score_min_loc}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
258 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
259 #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
260
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
261 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
262 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
263 --ma ${analysis_type.scoring_options.ma}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
264 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
265 --mp '${analysis_type.scoring_options.mp}'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
266 --np ${analysis_type.scoring_options.np}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
267 --rdg ${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
268 --rfg ${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
269 #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
270
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
271 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
272 -k ${analysis_type.reporting_options.k}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
273 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
274 -a
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
275 #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
276
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
277 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
278 -D ${analysis_type.effort_options.D}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
279 -R ${analysis_type.effort_options.R}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
280 #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
281
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
282 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
283 ${analysis_type.sam_options.no_unal}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
284 ${analysis_type.sam_options.omit_sec_seq}
20
dc1639b66f12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 1912a560c3ad87117f18570fcf3ba4af4f924340
iuc
parents: 19
diff changeset
285 ${analysis_type.sam_options.sam_no_qname_trunc}
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
286 ${analysis_type.sam_options.xeq}
20
dc1639b66f12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 1912a560c3ad87117f18570fcf3ba4af4f924340
iuc
parents: 19
diff changeset
287 ${analysis_type.sam_options.soft_clipped_unmapped_tlen}
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
288 #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
289
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
290 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
291 ${analysis_type.other_options.reorder}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
292 ${analysis_type.other_options.non_deterministic}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
293 --seed ${analysis_type.other_options.seed}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
294 #end if
4
1fc845afa3ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 32fe80982b5c59687eece667f0372002588566f8-dirty
devteam
parents: 3
diff changeset
295
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
296 #elif str( $analysis_type.analysis_type_selector ) == "cline":
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
297 ${analysis_type.cline}
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
298 #end if
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
299
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
300 ## mapping stats (i.e. stderr from bowtie2)
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
301 #if $save_mapping_stats
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
302 2> '$mapping_stats'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
303 #end if
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
304
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
305 ## output file
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
306 #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
307 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
308 #else
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
309 > '$output_sam'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
310 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
311
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
312 ## rename unaligned sequence files
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
313 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
314 #from os.path import splitext
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
315 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
316 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
317 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
318 #end if
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
319 #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r:
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
320 #from os.path import splitext
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
321 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
322 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
323 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
324 #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
325
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
326 ]]></command>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
327 <inputs>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
328 <!-- single/paired -->
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
329 <conditional name="library">
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
330 <param name="type" type="select" label="Is this single or paired library">
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
331 <option value="single">Single-end</option>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
332 <option value="paired">Paired-end</option>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
333 <option value="paired_collection">Paired-end Dataset Collection</option>
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
334 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
335 </param>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
336
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
337 <when value="single">
16
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
338 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
339 <expand macro="align_unalign" />
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
340 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
341 <when value="paired">
16
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
342 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #1" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
343 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #2" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
344 <expand macro="align_unalign" />
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
345 <expand macro="paired_end_options" />
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
346 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
347 <when value="paired_collection">
16
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
348 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
349 <expand macro="align_unalign" />
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
350 <expand macro="paired_end_options" />
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
351 </when>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
352 <when value="paired_interleaved">
16
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
353 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTQ file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;. --interleaved"/>
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
354 <expand macro="align_unalign" />
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
355 <expand macro="paired_end_options" />
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
356 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
357 </conditional>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
358 <!-- reference genome -->
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
359 <conditional name="reference_genome">
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
360 <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
361 <option value="indexed">Use a built-in genome index</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
362 <option value="history">Use a genome from the history and build index</option>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
363 </param>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
364 <when value="indexed">
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
365 <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
366 <options from_data_table="bowtie2_indexes">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
367 <filter type="sort_by" column="2"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
368 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
369 </options>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
370 </param>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
371 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
372 <when value="history">
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
373 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
374 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
375 </conditional>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
376 <!-- 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
377 <expand macro="read_group_conditional" />
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
378 <conditional name="analysis_type">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
379 <param name="analysis_type_selector" type="select" label="Select analysis mode">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
380 <option value="simple">1: Default setting only</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
381 <option value="full">2: Full parameter list</option>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
382 </param>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
383 <when value="simple">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
384 <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
385 <option value="no_presets" selected="True">No, just use defaults</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
386 <option value="--very-fast">Very fast end-to-end (--very-fast)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
387 <option value="--fast">Fast end-to-end (--fast)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
388 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
389 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
390 <option value="--very-fast-local">Very fast local (--very-fast-local)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
391 <option value="--fast-local">Fast local (--fast-local)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
392 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
393 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
394 </param>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
395 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
396 <when value="full">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
397 <conditional name="input_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
398 <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
399 <option value="yes">Yes</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
400 <option value="no" selected="true">No</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
401 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
402 <when value="yes">
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
403 <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
404 <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
405 <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
406 <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
407 <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
408 <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
409 <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
410 </param>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
411 <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
412 <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
413 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
414 <when value="no">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
415 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
416 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
417 </conditional>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
418 <conditional name="alignment_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
419 <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
420 <option value="yes">Yes</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
421 <option value="no" selected="true">No</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
422 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
423 <when value="yes">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
424 <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
425 <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
426 <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
427 <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
428 <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
429 <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"/>
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
430 <param name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" 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"/>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
431 <param name="nofw" type="boolean" truevalue="--nofw" falsevalue="" 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"/>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
432 <param name="norc" type="boolean" truevalue="--norc" falsevalue="" 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"/>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
433 <param name="no_1mm_upfront" type="boolean" truevalue="--no-1mm-upfront" falsevalue="" 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
434 <conditional name="align_mode">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
435 <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
436 <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
437 <option value="local">Local (--local)</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
438 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
439 <when value="end-to-end">
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
440 <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
441 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
442 <when value="local">
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
443 <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
444 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
445 </conditional>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
446 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
447 <when value="no">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
448 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
449 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
450 </conditional>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
451 <conditional name="scoring_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
452 <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
453 <option value="yes">Yes</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
454 <option value="no" selected="true">No</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
455 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
456 <when value="yes">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
457 <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
458 <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
459 <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
460 <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
461 <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
462 <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
463 <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
464 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
465 <when value="no">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
466 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
467 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
468 </conditional>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
469 <conditional name="reporting_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
470 <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
471 <option value="no" selected="true">No, do not set</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
472 <option value="k">Set -k option and enter -k value</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
473 <option value="a">Set -a option</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
474 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
475 <when value="no">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
476 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
477 </when>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
478 <when value="k">
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
479 <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
480 </when>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
481 <when value="a">
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
482 <!-- do nothing here; set -a flag on the command line-->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
483 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
484 </conditional>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
485 <conditional name="effort_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
486 <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
487 <option value="yes">Yes</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
488 <option value="no" selected="true">No</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
489 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
490 <when value="yes">
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
491 <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
492 <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
493 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
494 <when value="no">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
495 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
496 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
497 </conditional>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
498 <conditional name="sam_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
499 <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
500 <option value="yes">Yes</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
501 <option value="no" selected="true">No</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
502 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
503 <when value="yes">
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
504 <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
505 <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"/>
20
dc1639b66f12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 1912a560c3ad87117f18570fcf3ba4af4f924340
iuc
parents: 19
diff changeset
506 <param name="sam_no_qname_trunc" argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>
18
121110a12cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
507 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
20
dc1639b66f12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 1912a560c3ad87117f18570fcf3ba4af4f924340
iuc
parents: 19
diff changeset
508 <param name="soft_clipped_unmapped_tlen" argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
509 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
510 <when value="no">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
511 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
512 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
513 </conditional>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
514 <conditional name="other_options">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
515 <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
516 <option value="yes">Yes</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
517 <option value="no" selected="true">No</option>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
518 </param>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
519 <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
520 <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
521 <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
522 <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
523 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
524 <when value="no">
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
525 <!-- do nothing -->
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
526 </when>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
527 </conditional>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
528 <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
529 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
530 </conditional>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
531 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
532 </inputs>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
533 <!-- define outputs -->
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
534 <outputs>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
535 <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
536 <filter>library['unaligned_file'] is True</filter>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
537 <actions>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
538 <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
539 <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
540 <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
541 <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
542 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
543 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
544 <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
545 <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
546 <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
547 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
548 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
549 <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
550 <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
551 <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
552 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
553 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
554 </conditional>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
555 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
556 </data>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
557 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" >
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
558 <filter>library['aligned_file'] is True</filter>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
559 <actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
560 <conditional name="library.type">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
561 <when value="single">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
562 <action type="format">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
563 <option type="from_param" name="library.input_1" param_attribute="ext" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
564 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
565 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
566 <when value="paired">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
567 <action type="format">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
568 <option type="from_param" name="library.input_1" param_attribute="ext" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
569 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
570 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
571 <when value="paired_collection">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
572 <action type="format">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
573 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
574 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
575 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
576 </conditional>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
577 </actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
578 </data>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
579 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
580 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
581 <actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
582 <conditional name="library.type">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
583 <when value="paired">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
584 <action type="format">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
585 <option type="from_param" name="library.input_2" param_attribute="ext" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
586 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
587 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
588 <when value="paired_collection">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
589 <action type="format">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
590 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
591 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
592 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
593 </conditional>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
594 </actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
595 </data>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
596 <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
597 <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
598 <actions>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
599 <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
600 <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
601 <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
602 <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
603 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
604 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
605 <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
606 <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
607 <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
608 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
609 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
610 </conditional>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
611 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
612 </data>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
613 <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
614 <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
615 <actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
616 <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
617 <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
618 <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
619 <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
620 <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
621 <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
622 </option>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
623 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
624 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
625 <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
626 <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
627 <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
628 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
629 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
630 </conditional>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
631 </actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
632 </data>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
633 <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
634 <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
635 <actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
636 <conditional name="reference_genome.source">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
637 <when value="indexed">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
638 <action type="metadata" name="dbkey">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
639 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
640 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
641 <filter type="param_value" ref="reference_genome.index" column="0"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
642 </option>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
643 </action>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
644 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
645 <when value="history">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
646 <action type="metadata" name="dbkey">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
647 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
648 </action>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
649 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
650 </conditional>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
651 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
652 </data>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
653 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
654 <filter>save_mapping_stats is True</filter>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
655 </data>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
656 </outputs>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
657 <tests>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
658 <test>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
659 <!-- test on paired-end datasets -->
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
660 <param name="type" value="paired"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
661 <param name="paired_options_selector" value="no"/>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
662 <param name="unaligned_file" value="false"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
663 <param name="analysis_type_selector" value="simple"/>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
664 <param name="source" value="history" />
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
665 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
666 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
667 <param name="own_file" value="bowtie2-ref.fasta" />
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
668 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
669 </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
670 <test>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
671 <!-- test on paired collection -->
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
672 <param name="type" value="paired_collection"/>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
673 <param name="paired_options_selector" value="no"/>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
674 <param name="unaligned_file" value="false"/>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
675 <param name="analysis_type_selector" value="simple"/>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
676 <param name="source" value="history" />
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
677 <param name="input_1">
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
678 <collection type="paired">
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
679 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" />
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
680 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" />
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
681 </collection>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
682 </param>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
683 <param name="own_file" value="bowtie2-ref.fasta" />
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
684 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
685 </test>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
686 <test>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
687 <!-- test on paired-end datasets with read group info -->
5
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
688 <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
689 <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
690 <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
691 <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
692 <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
693 <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
694 <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
695 <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
696 <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
697 <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
698 <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
699 <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
700 </test>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
701 <test>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
702 <!-- test on paired-end datasets with stats output -->
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
703 <param name="type" value="paired"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
704 <param name="paired_options_selector" value="no"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
705 <param name="unaligned_file" value="false"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
706 <param name="analysis_type_selector" value="simple"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
707 <param name="source" value="history" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
708 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
709 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
710 <param name="own_file" value="bowtie2-ref.fasta" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
711 <param name="save_mapping_stats" value="true" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
712 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
713 <output name="mapping_stats">
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
714 <assert_contents>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
715 <has_text text="of these" />
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
716 </assert_contents>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
717 </output>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
718 </test>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
719 <test>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
720 <!-- test on interleaved dataset -->
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
721 <param name="type" value="paired_interleaved"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
722 <!-- <param name="paired_options_selector" value="no"/> -->
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
723 <param name="unaligned_file" value="false"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
724 <param name="analysis_type_selector" value="simple"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
725 <param name="rg_selector" value="set"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
726 <param name="ID" value="rg1"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
727 <param name="PL" value="CAPILLARY"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
728 <param name="source" value="history" />
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
729 <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/>
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
730 <param name="own_file" value="bowtie2-ref.fasta" />
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
731 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="2"/>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
732 </test>
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
733 <test>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
734 <!-- test on fastqsanger.gz paired-end datasets -->
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
735 <param name="type" value="paired"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
736 <param name="paired_options_selector" value="no"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
737 <param name="unaligned_file" value="false"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
738 <param name="analysis_type_selector" value="simple"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
739 <param name="source" value="history" />
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
740 <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
741 <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
742 <param name="own_file" value="bowtie2-ref.fasta" />
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
743 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
744 </test>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
745 <test>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
746 <!-- test on fastqsanger.bz2 paired-end datasets -->
14
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
747 <param name="type" value="paired"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
748 <param name="paired_options_selector" value="no"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
749 <param name="unaligned_file" value="false"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
750 <param name="analysis_type_selector" value="simple"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
751 <param name="source" value="history" />
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
752 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
753 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
754 <param name="own_file" value="bowtie2-ref.fasta" />
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
755 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
756 </test>
16
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
757 <test>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
758 <!-- test on fasta paired-end datasets -->
16
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
759 <param name="type" value="paired"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
760 <param name="paired_options_selector" value="no"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
761 <param name="unaligned_file" value="false"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
762 <param name="analysis_type_selector" value="simple"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
763 <param name="source" value="history" />
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
764 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
765 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
766 <param name="own_file" value="bowtie2-ref.fasta" />
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
767 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
8ccbdbe9a695 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
768 </test>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
769 </tests>
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
770 <help><![CDATA[
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
771 **Bowtie2 Overview**
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
772
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
773 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
774 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
775
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
776 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
777 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
778 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
779
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
780 -----
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
781
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
782 **Selecting reference genomes for Bowtie2**
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
783
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
784 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
785
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
786 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.
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
787 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.
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
788
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
789 If your genome of interest is not listed here you have two choices:
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
790
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
791 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
792 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
793
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
794 ------
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
795
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
796 .. class:: infomark
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
797
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
798 **Bowtie2 options**
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
799
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
800 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
801
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
802 -----
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
803
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
804 **Inputs**
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
805
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
806 Bowtie 2 accepts files in Sanger FASTQ format (single or paired-end). Paired-end data can represented as two individual (forward and reverse) datasets, as well as a single interleaved dataset (see an example at the end of the help section).
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
807
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
808 ------
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
809
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
810 **Input options**::
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
811
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
812 --interleaved
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
813 Reads interleaved FASTQ files where the first two records (8 lines) represent a mate pair.
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
814
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
815 -s/--skip <int>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
816 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
817
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
818 -u/--qupto <int>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
819 Align the first `<int>` reads or read pairs from the input (after the
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
820 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
821
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
822 -5/--trim5 <int>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
823 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
824
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
825 -3/--trim3 <int>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
826 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
827
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
828 --phred33
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
829 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
830 also called the "Phred+33" encoding, which is used by the very latest Illumina
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
831 pipelines.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
832
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
833 --phred64
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
834 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
835 also called the "Phred+64" encoding.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
836
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
837 --solexa-quals
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
838 Convert input qualities from Solexa Phred quality (which can be negative) to
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
839 Phred Phred quality (which can't). This scheme was used in older Illumina GA
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
840 Pipeline versions (prior to 1.3). Default: off.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
841
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
842 --int-quals
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
843 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
844 Integers are treated as being on the Phred quality scale unless
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
845 `--solexa-quals` is also specified. Default: off.
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
846
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
847 ------
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
848
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
849 **Presets in `--end-to-end` mode**::
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
850
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
851 --very-fast
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
852 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
853
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
854 --fast
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
855 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
856
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
857 --sensitive
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
858 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
859
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
860 --very-sensitive
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
861 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
862
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
863 ------
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
864
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
865 **Presets options in `--local` mode**::
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
866
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
867 --very-fast-local
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
868 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
869
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
870 --fast-local
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
871 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
872
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
873 --sensitive-local
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
874 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
875
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
876 --very-sensitive-local
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
877 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
878
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
879 ------
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
880
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
881 **Alignment options**::
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
882
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
883 -N <int>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
884 Sets the number of mismatches to allowed in a seed alignment during multiseed
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
885 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
886 (often much slower) but increases sensitivity. Default: 0.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
887
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
888 -L <int>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
889 Sets the length of the seed substrings to align during multiseed alignment.
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
890 Smaller values make alignment slower but more sensitive. Default: the
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
891 `--sensitive` preset is used by default, which sets `-L` to 22 in
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
892 `--end-to-end` mode and to 20 in `--local` mode.
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
893
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
894 -i <func>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
895 Sets a function governing the interval between seed substrings to use during
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
896 multiseed alignment. For instance, if the read has 30 characers, and seed
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
897 length is 10, and the seed interval is 6, the seeds extracted will be:
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
898
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
899 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
900 Seed 1 fw: TAGCTACGCT
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
901 Seed 1 rc: AGCGTAGCTA
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
902 Seed 2 fw: CGCTCTACGC
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
903 Seed 2 rc: GCGTAGAGCG
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
904 Seed 3 fw: ACGCTATCAT
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
905 Seed 3 rc: ATGATAGCGT
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
906 Seed 4 fw: TCATGCATAA
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
907 Seed 4 rc: TTATGCATGA
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
908
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
909 Since it's best to use longer intervals for longer reads, this parameter sets
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
910 the interval as a function of the read length, rather than a single
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
911 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
912 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
913 If the function returns a result less than
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
914 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
915 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
916 in `--local` mode.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
917
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
918 --n-ceil <func>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
919 Sets a function governing the maximum number of ambiguous characters (usually
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
920 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
921 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
922 where x is the read length. Reads exceeding this ceiling are filtered out.
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
923 Default: `L,0,0.15`.
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
924
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
925 --dpad <int>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
926 "Pads" dynamic programming problems by `<int>` columns on either side to allow
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
927 gaps. Default: 15.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
928
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
929 --gbar <int>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
930 Disallow gaps within `<int>` positions of the beginning or end of the read.
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
931 Default: 4.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
932
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
933 --ignore-quals
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
934 When calculating a mismatch penalty, always consider the quality value at the
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
935 mismatched position to be the highest possible, regardless of the actual value.
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
936 I.e. input is treated as though all quality values are high. This is also the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
937 default behavior when the input doesn't specify quality values (e.g. in `-f`,
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
938 `-r`, or `-c` modes).
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
939
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
940 --nofw/--norc
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
941 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
942 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
943 not attempt to align unpaired reads against the reverse-complement (Crick)
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
944 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
945 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
946 paired-end configurations corresponding to fragments from the reverse-complement
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
947 (Crick) strand. Default: both strands enabled.
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
948
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
949 --no-1mm-upfront
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
950 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
951 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
952 alignments can be found very quickly, and many short read alignments have exact or
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
953 near-exact end-to-end alignments. However, this can lead to unexpected
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
954 alignments when the user also sets options governing the multiseed heuristic,
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
955 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
956 to the length of the read, the user will be surprised to find 1-mismatch alignments
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
957 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
958 alignments before using the multiseed heuristic, which leads to the expected
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
959 behavior when combined with options such as `-L` and `-N`. This comes at the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
960 expense of speed.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
961
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
962 --end-to-end
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
963 In this mode, Bowtie 2 requires that the entire read align from one end to the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
964 other, without any trimming (or "soft clipping") of characters from either end.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
965 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
966 are less than or equal to 0, and the greatest possible alignment score is 0.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
967 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
968
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
969 --local
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
970 In this mode, Bowtie 2 does not require that the entire read align from one end
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
971 to the other. Rather, some characters may be omitted ("soft clipped") from the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
972 ends in order to achieve the greatest possible alignment score. The match bonus
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
973 `--ma` is used in this mode, and the best possible alignment score is equal to
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
974 the match bonus (`--ma`) times the length of the read. Specifying `--local`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
975 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
976 the local version of the preset (`--very-fast-local`). This is mutually
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
977 exclusive with `--end-to-end`. `--end-to-end` is the default mode.
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
978
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
979 -----
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
980
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
981 **Scoring options**::
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
982
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
983 --ma <int>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
984 Sets the match bonus. In `--local` mode `<int>` is added to the alignment
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
985 score for each position where a read character aligns to a reference character
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
986 and the characters match. Not used in `--end-to-end` mode. Default: 2.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
987
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
988 --mp MX,MN
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
989 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
990 number less than or equal to `MX` and greater than or equal to `MN` is
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
991 subtracted from the alignment score for each position where a read character
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
992 aligns to a reference character, the characters do not match, and neither is an
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
993 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
994 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
995 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
996
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
997 --np <int>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
998 Sets penalty for positions where the read, reference, or both, contain an
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
999 ambiguous character such as `N`. Default: 1.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1000
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1001 --rdg <int1>,<int2>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1002 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1003 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1004
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1005 --rfg <int1>,<int2>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1006 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1007 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1008 5, 3.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
1009
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1010 --score-min <func>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1011 Sets a function governing the minimum alignment score needed for an alignment to
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1012 be considered "valid" (i.e. good enough to report). This is a function of read
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1013 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
1014 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
1015 the default in `--local` mode is `G,20,8`.
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1016
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1017 -----
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1018
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1019 **Reporting options**::
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1020
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1021 -k <int>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1022 By default, `bowtie2` searches for distinct, valid alignments for each read.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1023 When it finds a valid alignment, it continues looking for alignments that are
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1024 nearly as good or better. The best alignment found is reported (randomly
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1025 selected from among best if tied). Information about the best alignments is
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1026 used to estimate mapping quality and to set SAM optional fields, such as
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1027 `AS:i` and `XS:i`.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1028
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1029 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1030 searches for at most `<int>` distinct, valid alignments for each read. The
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1031 search terminates when it can't find more distinct valid alignments, or when it
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1032 finds `<int>`, whichever happens first. All alignments found are reported in
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1033 descending order by alignment score. The alignment score for a paired-end
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1034 alignment equals the sum of the alignment scores of the individual mates. Each
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1035 reported read or pair alignment beyond the first has the SAM 'secondary' bit
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1036 (which equals 256) set in its FLAGS field. For reads that have more than
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1037 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1038 `<int>` alignments reported are the best possible in terms of alignment score.
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1039 `-k` is mutually exclusive with `-a`.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
1040
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1041 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1042 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1043
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1044 -a
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1045 Like `-k` but with no upper limit on number of alignments to search for. `-a`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1046 is mutually exclusive with `-k`.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1047
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1048 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1049 aligning reads to long, repetitive genomes this mode can be very, very slow.
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1050
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1051 -----
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1052
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1053 **Effort options**::
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1054
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1055 -D <int>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1056 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1057 moves on, using the alignments found so far. A seed extension "fails" if it
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1058 does not yield a new best or a new second-best alignment. This limit is
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1059 automatically adjusted up when -k or -a are specified. Default: 15.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1060
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1061 -R <int>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1062 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1063 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1064 (same length, same number of mismatches allowed) at different offsets and
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1065 searches for more alignments. A read is considered to have repetitive seeds if
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1066 the total number of seed hits divided by the number of seeds that aligned at
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1067 least once is greater than 300. Default: 2.
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1068
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1069 -----
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1070
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1071 **Paired-end options**::
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
1072
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1073 -I/--minins <int>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1074 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1075 specified and a paired-end alignment consists of two 20-bp alignments in the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1076 appropriate orientation with a 20-bp gap between them, that alignment is
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1077 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1078 be valid in that case. If trimming options `-3` or `-5` are also used, the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1079 `-I` constraint is applied with respect to the untrimmed mates.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1080
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1081 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1082 run. This is because larger differences bewteen `-I` and `-X` require that
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1083 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1084 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1085 efficient.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1086
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1087 Default: 0 (essentially imposing no minimum)
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1088
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1089 -X/--maxins <int>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1090 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1091 is specified and a paired-end alignment consists of two 20-bp alignments in the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1092 proper orientation with a 60-bp gap between them, that alignment is considered
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1093 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1094 that case. If trimming options `-3` or `-5` are also used, the `-X`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1095 constraint is applied with respect to the untrimmed mates, not the trimmed
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1096 mates.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1097
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1098 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1099 run. This is because larger differences bewteen `-I` and `-X` require that
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1100 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1101 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1102 efficient.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1103
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1104 Default: 500.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
1105
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1106 --fr/--rf/--ff
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1107 The upstream/downstream mate orientations for a valid paired-end alignment
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1108 against the forward reference strand. E.g., if `--fr` is specified and there is
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1109 a candidate paired-end alignment where mate 1 appears upstream of the reverse
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1110 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1111 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1112 complement of mate 1 and all other constraints are met, that too is valid.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1113 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1114 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1115 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1116 for Illumina's Paired-end Sequencing Assay).
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1117
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1118 --no-mixed
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1119 By default, when `bowtie2` cannot find a concordant or discordant alignment for
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1120 a pair, it then tries to find alignments for the individual mates. This option
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1121 disables that behavior.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
1122
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1123 --no-discordant
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1124 By default, `bowtie2` looks for discordant alignments if it cannot find any
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1125 concordant alignments. A discordant alignment is an alignment where both mates
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1126 align uniquely, but that does not satisfy the paired-end constraints
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1127 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1128
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1129 --dovetail
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1130 If the mates "dovetail", that is if one mate alignment extends past the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1131 beginning of the other such that the wrong mate begins upstream, consider that
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
1132 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1133
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1134 --no-contain
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1135 If one mate alignment contains the other, consider that to be non-concordant.
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
1136 Default: a mate can contain the other in a concordant alignment.
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1137
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1138 --no-overlap
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1139 If one mate alignment overlaps the other at all, consider that to be
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
1140 non-concordant. Default: mates can overlap in a concordant alignment.
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1141
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
1142 ------
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
1143
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1144 **SAM options**::
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
1145
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1146 --rg-id <text>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1147 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1148 printed, with `<text>` as the value associated with the `ID:` tag. It also
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1149 causes the `RG:Z:` extra field to be attached to each SAM output record, with
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1150 value set to `<text>`.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
1151
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1152 --rg <text>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1153 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1154 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
1155 must also be specified. This is because the `ID` tag is required by the SAM
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
1156 Specification. Specify `--rg` multiple times to set multiple fields. See the
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
1157 SAM Specification for details about what fields are legal.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
1158
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1159 --omit-sec-seq
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1160 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1161 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1162 in those fields instead.
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1163
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1164 -----
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
1165
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1166 **Other options**::
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
1167
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1168 --reorder
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1169 Guarantees that output SAM records are printed in an order corresponding to the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1170 order of the reads in the original input file, even when `-p` is set greater
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1171 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1172 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1173 not specified. Has no effect if `-p` is set to 1, since output order will
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1174 naturally correspond to input order in that case.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
1175
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1176 --seed <int>
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1177 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
1178
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1179 --non-deterministic
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1180 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1181 seeds the generator with a number derived from (a) the read name, (b) the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1182 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1183 option. This means that if two reads are identical (same name, same
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1184 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1185 for both, even if there was ambiguity. When `--non-deterministic` is specified,
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1186 Bowtie 2 re-initializes its pseudo-random generator for each read using the
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1187 current time. This means that Bowtie 2 will not necessarily report the same
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1188 alignment for two identical reads. This is counter-intuitive for some users,
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1189 but might be more appropriate in situations where the input consists of many
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1190 identical reads.
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
1191
15
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1192 -----
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1193
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1194
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1195 **Paired-end (and mate-pair) data in fastq format**
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1196
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1197 Paired end datasets can be represented as two individual datasets:
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1198
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1199 First dataset::
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1200
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1201 @1/1
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1202 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1203 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1204 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1205 @2/1
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1206 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1207 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1208 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1209
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1210 Second dataset::
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1211
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1212 @1/2
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1213 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1214 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1215 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1216 @2/2
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1217 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1218 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1219 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1220
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1221 Or a single *interleaved* dataset::
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1222
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1223 @1/1
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1224 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1225 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1226 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1227 @1/2
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1228 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1229 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1230 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1231 @2/1
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1232 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1233 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1234 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1235 @2/2
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1236 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1237 +
43d12513224b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1238 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1239 ]]></help>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
1240 <citations>
17
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
1241 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
1242 <citation type="doi">10.1038/nmeth.1923</citation>
66f992977578 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
1243 </citations>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
1244 </tool>