Mercurial > repos > devteam > bowtie2

annotate bowtie2_wrapper.xml @ 22:b2f8e8b8b9a3 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 fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
author iuc
date Thu, 12 Apr 2018 17:42:23 -0400
parents e798c0b3384c
children 5e52e98ff239
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
22
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
1 <tool id="bowtie2" name="Bowtie2" version="2.3.4.2" profile="18.01">
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
2 <description>- map reads against reference genome</description>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
3 <macros>
15
7e0b333f39e1 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
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
5 </macros>
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
6 <requirements>
19
7f9d1892eb1b 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>
22
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
8 <requirement type="package" version="1.8">samtools</requirement>
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
9 </requirements>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
10 <version_command>bowtie2 --version</version_command>
11
fa69d5a7b8c8 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[
21
e798c0b3384c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
iuc
parents: 20
diff changeset
12 ## Use pipefail if available to quit with first non-zero exit code
e798c0b3384c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
iuc
parents: 20
diff changeset
13 set -o | grep -q pipefail && set -o pipefail;
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
14 ## prepare bowtie2 index
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
15 #set index_path = ''
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
16 #if str($reference_genome.source) == "history":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
17 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome &&
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
18 ln -s -f '$reference_genome.own_file' genome.fa &&
e0ca9500999b 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 = 'genome'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
20 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
21 #set index_path = $reference_genome.index.fields.path
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
22 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
23
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
24 ## Link in the input files, so bowtie2 can tell their type
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
25
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
26 #set compressed="False"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
27 #set reads_are_fastq = True
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
28 #if str($library.type) == 'paired':
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
29 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
30 #set read1 = "input_f.fastq.gz"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
31 #set compressed = "GZ"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
32 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
33 #set read1 = "input_f.fastq.bz2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
34 #set compressed = "BZ2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
35 #else if $library.input_1.is_of_type('fasta'):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
36 #set reads_are_fastq = False
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
37 #set read1 = "input_f.fasta"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
38 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
39 #set read1 = "input_f.fastq"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
40 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
41 ln -f -s '${library.input_1}' ${read1} &&
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
42
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
43 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
44 #set read2 = "input_r.fastq.gz"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
45 #set compressed = "GZ"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
46 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
47 #set read2 = "input_r.fastq.bz2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
48 #set compressed = "BZ2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
49 #else if $library.input_2.is_of_type('fasta'):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
50 #set read2 = "input_r.fasta"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
51 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
52 #set read2 = "input_r.fastq"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
53 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
54 ln -f -s '${library.input_2}' ${read2} &&
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
55 #else if str($library.type) == 'paired_collection':
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
56 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
57 #set read1 = "input_f.fastq.gz"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
58 #set compressed = "GZ"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
59 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
60 #set read1 = "input_f.fastq.bz2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
61 #set compressed = "BZ2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
62 #else if $library.input_1.forward.is_of_type('fasta'):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
63 #set reads_are_fastq = False
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
64 #set read1 = "input_f.fasta"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
65 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
66 #set read1 = "input_f.fastq"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
67 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
68 ln -s '${library.input_1.forward}' ${read1} &&
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
69
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
70 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
71 #set read2 = "input_r.fastq.gz"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
72 #set compressed = "GZ"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
73 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
74 #set read2 = "input_r.fastq.bz2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
75 #set compressed = "BZ2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
76 #else if $library.input_1.reverse.is_of_type("fasta"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
77 #set read2 = "input_r.fasta"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
78 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
79 #set read2 = "input_r.fastq"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
80 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
81 ln -s '${library.input_1.reverse}' ${read2} &&
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
82
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
83 #else if str($library.type) == 'paired_interleaved':
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
84 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
85 #set read1 = "input_il.fastq.gz"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
86 #set compressed = "GZ"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
87 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
88 #set read1 = "input_il.fastq.bz2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
89 #set compressed = "BZ2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
90 #else if $library.input_1.is_of_type("fasta"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
91 #set reads_are_fastq = False
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
92 #set read1 = "input_il.fasta"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
93 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
94 #set read1 = "input_il.fastq"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
95 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
96 ln -s '${library.input_1}' ${read1} &&
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
97 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
98 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
99 #set read1 = "input_f.fastq.gz"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
100 #set compressed = "GZ"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
101 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
102 #set read1 = "input_f.fastq.bz2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
103 #set compressed = "BZ2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
104 #else if $library.input_1.is_of_type("fasta"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
105 #set reads_are_fastq = False
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
106 #set read1 = "input_f.fasta"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
107 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
108 #set read1 = "input_f.fastq"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
109 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
110 ln -s '${library.input_1}' ${read1} &&
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
111 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
112
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
113 ## execute bowtie2
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
114
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
115 bowtie2
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
116
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
117 ## number of threads
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
118 -p \${GALAXY_SLOTS:-4}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
119
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
120 ## index file path
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
121 -x '$index_path'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
122
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
123 ## Input reads are fasta?
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
124 #if not reads_are_fastq:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
125 -f
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
126 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
127
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
128 ## Input reads
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
129 #if str( $library.type ) == "single":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
130 -U '${read1}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
131 #if str( $library.unaligned_file ) == "true":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
132 #if $compressed == "GZ":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
133 --un-gz '${output_unaligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
134 #else if $compressed == "BZ2":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
135 --un-bz2 '${output_unaligned_reads_l}'
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
136 #else:
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
137 --un '${output_unaligned_reads_l}'
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
138 #end if
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
139 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
140 #if str( $library.aligned_file ) == "true":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
141 #if $compressed == "GZ":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
142 --al-gz '${output_aligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
143 #else if $compressed == "BZ2":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
144 --al-bz2 '${output_aligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
145 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
146 --al '${output_aligned_reads_l}'
16
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
147 #end if
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
148 #end if
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
149
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
150 #elif str( $library.type ) == "paired_interleaved":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
151 --interleaved '${read1}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
152 #if str( $library.unaligned_file ) == "true":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
153 #if $compressed == "GZ":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
154 --un-gz '${output_unaligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
155 #else if $compressed == "BZ2":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
156 --un-bz2 '${output_unaligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
157 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
158 --un '${output_unaligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
159 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
160 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
161 #if str( $library.aligned_file ) == "true":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
162 #if $compressed == "GZ":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
163 --al-gz '${output_aligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
164 #else if $compressed == "BZ2":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
165 --al-bz2 '${output_aligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
166 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
167 --al '${output_aligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
168 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
169 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
170 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
171 -1 '${read1}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
172 -2 '${read2}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
173 #if str( $library.unaligned_file ) == "true":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
174 #if $compressed == "GZ":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
175 --un-conc-gz '${output_unaligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
176 #else if $compressed == "BZ2":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
177 --un-conc-bz2 '${output_unaligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
178 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
179 --un-conc '${output_unaligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
180 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
181 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
182 #if str( $library.aligned_file ) == "true":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
183 #if $compressed == "GZ":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
184 --al-conc-gz '${output_aligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
185 #else if $compressed == "BZ2":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
186 --al-conc-bz2 '${output_aligned_reads_l}'
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
187 #else:
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
188 --al-conc '${output_aligned_reads_l}'
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
189 #end if
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
190 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
191 #if str( $library.paired_options.paired_options_selector ) == "yes":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
192 -I ${library.paired_options.I}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
193 -X ${library.paired_options.X}
e0ca9500999b 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.fr_rf_ff}
e0ca9500999b 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.no_mixed}
e0ca9500999b 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_discordant}
e0ca9500999b 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.dovetail}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
198 ${library.paired_options.no_contain}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
199 ${library.paired_options.no_overlap}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
200 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
201 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
202
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
203 ## Read group information.
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
204 @define_read_group_helpers@
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
205 #if str( $library.type ) == "single":
e0ca9500999b 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)
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
207 #elif str( $library.type ) == "paired":
e0ca9500999b 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, $library.input_2)
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
209 #else
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
210 #set $rg_auto_name = $read_group_name_default($library.input_1)
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
211 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
212 @set_use_rg_var@
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
213 @set_read_group_vars@
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
214 #if $use_rg
e0ca9500999b 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("", $rg_id, '"', arg='--rg-id ')
e0ca9500999b 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("SM:", $rg_sm, '"', arg='--rg ')
e0ca9500999b 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("PL:", $rg_pl, '"', arg='--rg ')
e0ca9500999b 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("LB:", $rg_lb, '"', arg='--rg ')
e0ca9500999b 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("CN:", $rg_cn, '"', arg='--rg ')
e0ca9500999b 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("DS:", $rg_ds, '"', arg='--rg ')
e0ca9500999b 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("DT:", $rg_dt, '"', arg='--rg ')
e0ca9500999b 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("FO:", $rg_fo, '"', arg='--rg ')
e0ca9500999b 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("KS:", $rg_ks, '"', arg='--rg ')
e0ca9500999b 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("PG:", $rg_pg, '"', arg='--rg ')
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
225 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
226 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
227 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
228
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
229 ## Analysis type
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
230 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
231 $analysis_type.presets
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
232 #elif str( $analysis_type.analysis_type_selector ) == "full":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
233 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
234 --skip ${analysis_type.input_options.skip}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
235 --qupto ${analysis_type.input_options.qupto}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
236 --trim5 ${analysis_type.input_options.trim5}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
237 --trim3 ${analysis_type.input_options.trim3}
e0ca9500999b 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.qv_encoding}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
239 ${analysis_type.input_options.solexa_quals}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
240 ${analysis_type.input_options.int_quals}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
241 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
242
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
243 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
244 -N ${analysis_type.alignment_options.N}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
245 -L ${analysis_type.alignment_options.L}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
246 -i '${analysis_type.alignment_options.i}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
247 --n-ceil '${analysis_type.alignment_options.n_ceil}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
248 --dpad ${analysis_type.alignment_options.dpad}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
249 --gbar ${analysis_type.alignment_options.gbar}
e0ca9500999b 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.ignore_quals}
e0ca9500999b 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.nofw}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
252 ${analysis_type.alignment_options.norc}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
253 ${analysis_type.alignment_options.no_1mm_upfront}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
254 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
255 --end-to-end
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
256 --score-min '${analysis_type.alignment_options.align_mode.score_min_ete}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
257 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
258 --local
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
259 --score-min '${analysis_type.alignment_options.align_mode.score_min_loc}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
260 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
261 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
262
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
263 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
264 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
265 --ma ${analysis_type.scoring_options.ma}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
266 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
267 --mp '${analysis_type.scoring_options.mp}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
268 --np ${analysis_type.scoring_options.np}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
269 --rdg ${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
270 --rfg ${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
271 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
272
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
273 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
274 -k ${analysis_type.reporting_options.k}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
275 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
276 -a
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
277 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
278
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
279 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
280 -D ${analysis_type.effort_options.D}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
281 -R ${analysis_type.effort_options.R}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
282 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
283 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
284 ${analysis_type.other_options.reorder}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
285 ${analysis_type.other_options.non_deterministic}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
286 --seed ${analysis_type.other_options.seed}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
287 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
288
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
289 #elif str( $analysis_type.analysis_type_selector ) == "cline":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
290 ${analysis_type.cline}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
291 #end if
10
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
292
22
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
293 #if str( $sam_options.sam_options_selector ) == "yes":
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
294 ${sam_options.no_unal}
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
295 ${sam_options.omit_sec_seq}
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
296 ${sam_options.sam_no_qname_trunc}
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
297 ${sam_options.xeq}
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
298 ${sam_options.soft_clipped_unmapped_tlen}
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
299 ${sam_options.reorder}
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
300 #end if
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
301
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
302 ## mapping stats (i.e. stderr from bowtie2)
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
303 #if $save_mapping_stats
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
304 2> '$mapping_stats'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
305 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
306
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
307 ## output file
22
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
308 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
309 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output'
22
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
310 #else if $sam_options.reorder:
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
311 | samtools view -bS - -o '$output'
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
312 #else:
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
313 > '$output_sam'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
314 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
315
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
316 ## rename unaligned sequence files
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
317 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
318 #from os.path import splitext
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
319 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
320 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
321 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
322 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
323 #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
324 #from os.path import splitext
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
325 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
326 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
327 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
328 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
329
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
330 ]]></command>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
331 <inputs>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
332 <!-- single/paired -->
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
333 <conditional name="library">
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
334 <param name="type" type="select" label="Is this single or paired library">
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
335 <option value="single">Single-end</option>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
336 <option value="paired">Paired-end</option>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
337 <option value="paired_collection">Paired-end Dataset Collection</option>
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
338 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
339 </param>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
340
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
341 <when value="single">
16
def46fdb3909 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" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
343 <expand macro="align_unalign" />
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
344 </when>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
345 <when value="paired">
16
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
346 <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;" />
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
347 <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
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
348 <expand macro="align_unalign" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
349 <expand macro="paired_end_options" />
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
350 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
351 <when value="paired_collection">
16
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
352 <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
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
353 <expand macro="align_unalign" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
354 <expand macro="paired_end_options" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
355 </when>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
356 <when value="paired_interleaved">
16
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
357 <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
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
358 <expand macro="align_unalign" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
359 <expand macro="paired_end_options" />
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
360 </when>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
361 </conditional>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
362 <!-- reference genome -->
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
363 <conditional name="reference_genome">
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
364 <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">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
365 <option value="indexed">Use a built-in genome index</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
366 <option value="history">Use a genome from the history and build index</option>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
367 </param>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
368 <when value="indexed">
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
369 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
370 <options from_data_table="bowtie2_indexes">
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
371 <filter type="sort_by" column="2"/>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
372 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
373 </options>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
374 </param>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
375 </when>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
376 <when value="history">
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
377 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
378 </when>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
379 </conditional>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
380 <!-- read group settings -->
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
381 <expand macro="read_group_conditional" />
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
382 <conditional name="analysis_type">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
383 <param name="analysis_type_selector" type="select" label="Select analysis mode">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
384 <option value="simple">1: Default setting only</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
385 <option value="full">2: Full parameter list</option>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
386 </param>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
387 <when value="simple">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
388 <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.">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
389 <option value="no_presets" selected="True">No, just use defaults</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
390 <option value="--very-fast">Very fast end-to-end (--very-fast)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
391 <option value="--fast">Fast end-to-end (--fast)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
392 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
393 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
394 <option value="--very-fast-local">Very fast local (--very-fast-local)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
395 <option value="--fast-local">Fast local (--fast-local)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
396 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
397 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
398 </param>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
399 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
400 <when value="full">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
401 <conditional name="input_options">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
402 <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">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
403 <option value="yes">Yes</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
404 <option value="no" selected="true">No</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
405 </param>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
406 <when value="yes">
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
407 <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"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
408 <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
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
409 <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"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
410 <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"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
411 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
412 <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>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
413 <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
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
414 </param>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
415 <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"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
416 <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
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
417 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
418 <when value="no">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
419 <!-- do nothing -->
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
420 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
421 </conditional>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
422 <conditional name="alignment_options">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
423 <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">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
424 <option value="yes">Yes</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
425 <option value="no" selected="true">No</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
426 </param>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
427 <when value="yes">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
428 <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"/>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
429 <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"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
430 <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`"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
431 <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`"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
432 <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
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
433 <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
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
434 <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"/>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
435 <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"/>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
436 <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"/>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
437 <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
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
438 <conditional name="align_mode">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
439 <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">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
440 <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
441 <option value="local">Local (--local)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
442 </param>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
443 <when value="end-to-end">
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
444 <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
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
445 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
446 <when value="local">
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
447 <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
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
448 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
449 </conditional>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
450 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
451 <when value="no">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
452 <!-- do nothing -->
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
453 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
454 </conditional>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
455 <conditional name="scoring_options">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
456 <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">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
457 <option value="yes">Yes</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
458 <option value="no" selected="true">No</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
459 </param>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
460 <when value="yes">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
461 <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"/>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
462 <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
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
463 <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"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
464 <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"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
465 <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"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
466 <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"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
467 <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"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
468 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
469 <when value="no">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
470 <!-- do nothing -->
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
471 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
472 </conditional>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
473 <conditional name="reporting_options">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
474 <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">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
475 <option value="no" selected="true">No, do not set</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
476 <option value="k">Set -k option and enter -k value</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
477 <option value="a">Set -a option</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
478 </param>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
479 <when value="no">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
480 <!-- do nothing -->
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
481 </when>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
482 <when value="k">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
483 <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
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
484 </when>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
485 <when value="a">
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
486 <!-- do nothing here; set -a flag on the command line-->
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
487 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
488 </conditional>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
489 <conditional name="effort_options">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
490 <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">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
491 <option value="yes">Yes</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
492 <option value="no" selected="true">No</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
493 </param>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
494 <when value="yes">
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
495 <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
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
496 <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"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
497 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
498 <when value="no">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
499 <!-- do nothing -->
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
500 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
501 </conditional>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
502 <conditional name="other_options">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
503 <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">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
504 <option value="yes">Yes</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
505 <option value="no" selected="true">No</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
506 </param>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
507 <when value="yes">
22
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
508 <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. If selected output file will not be coordinate sorted." help="--reorder; Default=False"/>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
509 <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"/>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
510 <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
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
511 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
512 <when value="no">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
513 <!-- do nothing -->
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
514 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
515 </conditional>
22
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
516 </when>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
517 </conditional>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
518 <conditional name="sam_options">
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
519 <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">
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
520 <option value="yes">Yes</option>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
521 <option value="no" selected="true">No</option>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
522 </param>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
523 <when value="yes">
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
524 <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."/>
22
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
525 <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"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
526 <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"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
527 <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"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
528 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
529 <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"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
530 <param name="reorder" argument="--reorder" type="boolean" truevalue="--reorder" falsevalue=""
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
531 label="Reorder output to reflect order of the input file"
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
532 help="Reorder guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when -p is set greater than 1." />
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
533 </when>
22
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
534 <when value="no"/>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
535 </conditional>
10
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
536 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
537 </inputs>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
538 <!-- define outputs -->
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
539 <outputs>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
540 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
541 <filter>library['unaligned_file'] is True</filter>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
542 <actions>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
543 <conditional name="library.type">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
544 <when value="single">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
545 <action type="format">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
546 <option type="from_param" name="library.input_1" param_attribute="ext" />
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
547 </action>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
548 </when>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
549 <when value="paired">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
550 <action type="format">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
551 <option type="from_param" name="library.input_1" param_attribute="ext" />
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
552 </action>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
553 </when>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
554 <when value="paired_collection">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
555 <action type="format">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
556 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
557 </action>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
558 </when>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
559 </conditional>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
560 </actions>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
561 </data>
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
562 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" >
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
563 <filter>library['aligned_file'] is True</filter>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
564 <actions>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
565 <conditional name="library.type">
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
566 <when value="single">
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
567 <action type="format">
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
568 <option type="from_param" name="library.input_1" param_attribute="ext" />
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
569 </action>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
570 </when>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
571 <when value="paired">
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
572 <action type="format">
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
573 <option type="from_param" name="library.input_1" param_attribute="ext" />
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
574 </action>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
575 </when>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
576 <when value="paired_collection">
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
577 <action type="format">
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
578 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
579 </action>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
580 </when>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
581 </conditional>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
582 </actions>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
583 </data>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
584 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)">
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
585 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
586 <actions>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
587 <conditional name="library.type">
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
588 <when value="paired">
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
589 <action type="format">
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
590 <option type="from_param" name="library.input_2" param_attribute="ext" />
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
591 </action>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
592 </when>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
593 <when value="paired_collection">
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
594 <action type="format">
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
595 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
596 </action>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
597 </when>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
598 </conditional>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
599 </actions>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
600 </data>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
601 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
602 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
603 <actions>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
604 <conditional name="library.type">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
605 <when value="paired">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
606 <action type="format">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
607 <option type="from_param" name="library.input_2" param_attribute="ext" />
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
608 </action>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
609 </when>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
610 <when value="paired_collection">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
611 <action type="format">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
612 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
613 </action>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
614 </when>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
615 </conditional>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
616 </actions>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
617 </data>
22
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
618 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (BAM)">
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
619 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
22
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
620 <change_format>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
621 <when input="sam_options.reorder" value="--reorder" format="qname_input_sorted.bam" />
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
622 </change_format>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
623 <actions>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
624 <conditional name="reference_genome.source">
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
625 <when value="indexed">
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
626 <action type="metadata" name="dbkey">
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
627 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
628 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
629 <filter type="param_value" ref="reference_genome.index" column="0"/>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
630 </option>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
631 </action>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
632 </when>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
633 <when value="history">
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
634 <action type="metadata" name="dbkey">
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
635 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
636 </action>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
637 </when>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
638 </conditional>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
639 </actions>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
640 </data>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
641 <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
642 <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
643 <actions>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
644 <conditional name="reference_genome.source">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
645 <when value="indexed">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
646 <action type="metadata" name="dbkey">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
647 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
648 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
649 <filter type="param_value" ref="reference_genome.index" column="0"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
650 </option>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
651 </action>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
652 </when>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
653 <when value="history">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
654 <action type="metadata" name="dbkey">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
655 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
656 </action>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
657 </when>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
658 </conditional>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
659 </actions>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
660 </data>
10
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
661 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
662 <filter>save_mapping_stats is True</filter>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
663 </data>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
664 </outputs>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
665 <tests>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
666 <test>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
667 <!-- test on paired-end datasets -->
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
668 <param name="type" value="paired"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
669 <param name="paired_options_selector" value="no"/>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
670 <param name="unaligned_file" value="false"/>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
671 <param name="analysis_type_selector" value="simple"/>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
672 <param name="source" value="history" />
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
673 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
674 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
675 <param name="own_file" value="bowtie2-ref.fasta" />
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
676 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
677 </test>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
678 <test>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
679 <!-- test on paired collection -->
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
680 <param name="type" value="paired_collection"/>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
681 <param name="paired_options_selector" value="no"/>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
682 <param name="unaligned_file" value="false"/>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
683 <param name="analysis_type_selector" value="simple"/>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
684 <param name="source" value="history" />
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
685 <param name="input_1">
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
686 <collection type="paired">
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
687 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" />
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
688 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" />
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
689 </collection>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
690 </param>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
691 <param name="own_file" value="bowtie2-ref.fasta" />
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
692 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
693 </test>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
694 <test>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
695 <!-- test on paired-end datasets with read group info -->
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
696 <param name="type" value="paired"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
697 <param name="paired_options_selector" value="no"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
698 <param name="unaligned_file" value="false"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
699 <param name="analysis_type_selector" value="simple"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
700 <param name="rg_selector" value="set"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
701 <param name="ID" value="rg1"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
702 <param name="PL" value="CAPILLARY"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
703 <param name="source" value="history" />
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
704 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
705 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
706 <param name="own_file" value="bowtie2-ref.fasta" />
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
707 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
708 </test>
10
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
709 <test>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
710 <!-- test on paired-end datasets with stats output -->
10
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
711 <param name="type" value="paired"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
712 <param name="paired_options_selector" value="no"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
713 <param name="unaligned_file" value="false"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
714 <param name="analysis_type_selector" value="simple"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
715 <param name="source" value="history" />
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
716 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
717 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
718 <param name="own_file" value="bowtie2-ref.fasta" />
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
719 <param name="save_mapping_stats" value="true" />
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
720 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
721 <output name="mapping_stats">
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
722 <assert_contents>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
723 <has_text text="of these" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
724 </assert_contents>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
725 </output>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
726 </test>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
727 <test>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
728 <!-- test on interleaved dataset -->
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
729 <param name="type" value="paired_interleaved"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
730 <!-- <param name="paired_options_selector" value="no"/> -->
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
731 <param name="unaligned_file" value="false"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
732 <param name="analysis_type_selector" value="simple"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
733 <param name="rg_selector" value="set"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
734 <param name="ID" value="rg1"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
735 <param name="PL" value="CAPILLARY"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
736 <param name="source" value="history" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
737 <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
738 <param name="own_file" value="bowtie2-ref.fasta" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
739 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="2"/>
10
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
740 </test>
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
741 <test>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
742 <!-- test on fastqsanger.gz paired-end datasets -->
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
743 <param name="type" value="paired"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
744 <param name="paired_options_selector" value="no"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
745 <param name="unaligned_file" value="false"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
746 <param name="analysis_type_selector" value="simple"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
747 <param name="source" value="history" />
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
748 <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
749 <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
750 <param name="own_file" value="bowtie2-ref.fasta" />
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
751 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
752 </test>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
753 <test>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
754 <!-- test on fastqsanger.bz2 paired-end datasets -->
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
755 <param name="type" value="paired"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
756 <param name="paired_options_selector" value="no"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
757 <param name="unaligned_file" value="false"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
758 <param name="analysis_type_selector" value="simple"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
759 <param name="source" value="history" />
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
760 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
761 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
762 <param name="own_file" value="bowtie2-ref.fasta" />
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
763 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
764 </test>
16
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
765 <test>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
766 <!-- test on fasta paired-end datasets -->
16
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
767 <param name="type" value="paired"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
768 <param name="paired_options_selector" value="no"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
769 <param name="unaligned_file" value="false"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
770 <param name="analysis_type_selector" value="simple"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
771 <param name="source" value="history" />
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
772 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
773 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
774 <param name="own_file" value="bowtie2-ref.fasta" />
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
775 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
776 </test>
22
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
777 <test>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
778 <!-- test on fasta paired-end datasets with bam_native as output -->
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
779 <param name="type" value="paired"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
780 <param name="paired_options_selector" value="no"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
781 <param name="unaligned_file" value="false"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
782 <param name="analysis_type_selector" value="simple"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
783 <param name="source" value="history" />
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
784 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
785 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
786 <param name="own_file" value="bowtie2-ref.fasta" />
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
787 <param name="sam_options_selector" value="yes" />
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
788 <param name="reorder" value="true" />
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
789 <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" compare="sim_size"/>
b2f8e8b8b9a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
iuc
parents: 21
diff changeset
790 </test>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
791 </tests>
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
792 <help><![CDATA[
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
793 **Bowtie2 Overview**
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
794
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
795 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.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
796 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
797
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
798 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
799 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
800 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
801
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
802 -----
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
803
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
804 **Selecting reference genomes for Bowtie2**
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
805
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
806 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
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
807
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
808 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
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
809 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
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
810
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
811 If your genome of interest is not listed here you have two choices:
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
812
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
813 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
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
814 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
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
815
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
816 ------
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
817
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
818 .. class:: infomark
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
819
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
820 **Bowtie2 options**
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
821
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
822 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
823
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
824 -----
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
825
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
826 **Inputs**
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
827
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
828 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
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
829
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
830 ------
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
831
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
832 **Input options**::
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
833
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
834 --interleaved
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
835 Reads interleaved FASTQ files where the first two records (8 lines) represent a mate pair.
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
836
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
837 -s/--skip <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
838 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
839
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
840 -u/--qupto <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
841 Align the first `<int>` reads or read pairs from the input (after the
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
842 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
843
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
844 -5/--trim5 <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
845 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
846
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
847 -3/--trim3 <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
848 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
849
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
850 --phred33
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
851 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
852 also called the "Phred+33" encoding, which is used by the very latest Illumina
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
853 pipelines.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
854
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
855 --phred64
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
856 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
857 also called the "Phred+64" encoding.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
858
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
859 --solexa-quals
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
860 Convert input qualities from Solexa Phred quality (which can be negative) to
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
861 Phred Phred quality (which can't). This scheme was used in older Illumina GA
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
862 Pipeline versions (prior to 1.3). Default: off.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
863
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
864 --int-quals
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
865 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`....
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
866 Integers are treated as being on the Phred quality scale unless
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
867 `--solexa-quals` is also specified. Default: off.
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
868
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
869 ------
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
870
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
871 **Presets in `--end-to-end` mode**::
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
872
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
873 --very-fast
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
874 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
875
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
876 --fast
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
877 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
878
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
879 --sensitive
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
880 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
881
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
882 --very-sensitive
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
883 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
884
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
885 ------
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
886
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
887 **Presets options in `--local` mode**::
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
888
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
889 --very-fast-local
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
890 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00`
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
891
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
892 --fast-local
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
893 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75`
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
894
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
895 --sensitive-local
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
896 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
897
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
898 --very-sensitive-local
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
899 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
900
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
901 ------
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
902
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
903 **Alignment options**::
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
904
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
905 -N <int>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
906 Sets the number of mismatches to allowed in a seed alignment during multiseed
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
907 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
908 (often much slower) but increases sensitivity. Default: 0.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
909
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
910 -L <int>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
911 Sets the length of the seed substrings to align during multiseed alignment.
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
912 Smaller values make alignment slower but more sensitive. Default: the
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
913 `--sensitive` preset is used by default, which sets `-L` to 22 in
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
914 `--end-to-end` mode and to 20 in `--local` mode.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
915
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
916 -i <func>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
917 Sets a function governing the interval between seed substrings to use during
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
918 multiseed alignment. For instance, if the read has 30 characers, and seed
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
919 length is 10, and the seed interval is 6, the seeds extracted will be:
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
920
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
921 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
922 Seed 1 fw: TAGCTACGCT
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
923 Seed 1 rc: AGCGTAGCTA
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
924 Seed 2 fw: CGCTCTACGC
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
925 Seed 2 rc: GCGTAGAGCG
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
926 Seed 3 fw: ACGCTATCAT
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
927 Seed 3 rc: ATGATAGCGT
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
928 Seed 4 fw: TCATGCATAA
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
929 Seed 4 rc: TTATGCATGA
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
930
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
931 Since it's best to use longer intervals for longer reads, this parameter sets
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
932 the interval as a function of the read length, rather than a single
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
933 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
934 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length.
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
935 If the function returns a result less than
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
936 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
937 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
938 in `--local` mode.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
939
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
940 --n-ceil <func>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
941 Sets a function governing the maximum number of ambiguous characters (usually
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
942 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
943 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
944 where x is the read length. Reads exceeding this ceiling are filtered out.
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
945 Default: `L,0,0.15`.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
946
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
947 --dpad <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
948 "Pads" dynamic programming problems by `<int>` columns on either side to allow
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
949 gaps. Default: 15.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
950
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
951 --gbar <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
952 Disallow gaps within `<int>` positions of the beginning or end of the read.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
953 Default: 4.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
954
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
955 --ignore-quals
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
956 When calculating a mismatch penalty, always consider the quality value at the
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
957 mismatched position to be the highest possible, regardless of the actual value.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
958 I.e. input is treated as though all quality values are high. This is also the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
959 default behavior when the input doesn't specify quality values (e.g. in `-f`,
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
960 `-r`, or `-c` modes).
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
961
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
962 --nofw/--norc
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
963 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
964 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
965 not attempt to align unpaired reads against the reverse-complement (Crick)
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
966 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
967 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
968 paired-end configurations corresponding to fragments from the reverse-complement
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
969 (Crick) strand. Default: both strands enabled.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
970
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
971 --no-1mm-upfront
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
972 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
973 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
974 alignments can be found very quickly, and many short read alignments have exact or
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
975 near-exact end-to-end alignments. However, this can lead to unexpected
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
976 alignments when the user also sets options governing the multiseed heuristic,
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
977 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
978 to the length of the read, the user will be surprised to find 1-mismatch alignments
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
979 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
980 alignments before using the multiseed heuristic, which leads to the expected
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
981 behavior when combined with options such as `-L` and `-N`. This comes at the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
982 expense of speed.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
983
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
984 --end-to-end
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
985 In this mode, Bowtie 2 requires that the entire read align from one end to the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
986 other, without any trimming (or "soft clipping") of characters from either end.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
987 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
988 are less than or equal to 0, and the greatest possible alignment score is 0.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
989 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
990
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
991 --local
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
992 In this mode, Bowtie 2 does not require that the entire read align from one end
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
993 to the other. Rather, some characters may be omitted ("soft clipped") from the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
994 ends in order to achieve the greatest possible alignment score. The match bonus
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
995 `--ma` is used in this mode, and the best possible alignment score is equal to
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
996 the match bonus (`--ma`) times the length of the read. Specifying `--local`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
997 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
998 the local version of the preset (`--very-fast-local`). This is mutually
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
999 exclusive with `--end-to-end`. `--end-to-end` is the default mode.
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1000
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1001 -----
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1002
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1003 **Scoring options**::
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1004
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1005 --ma <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1006 Sets the match bonus. In `--local` mode `<int>` is added to the alignment
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1007 score for each position where a read character aligns to a reference character
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1008 and the characters match. Not used in `--end-to-end` mode. Default: 2.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1009
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1010 --mp MX,MN
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1011 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1012 number less than or equal to `MX` and greater than or equal to `MN` is
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1013 subtracted from the alignment score for each position where a read character
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1014 aligns to a reference character, the characters do not match, and neither is an
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1015 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1016 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1017 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1018
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1019 --np <int>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1020 Sets penalty for positions where the read, reference, or both, contain an
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1021 ambiguous character such as `N`. Default: 1.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1022
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1023 --rdg <int1>,<int2>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1024 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1025 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1026
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1027 --rfg <int1>,<int2>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1028 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1029 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1030 5, 3.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1031
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1032 --score-min <func>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1033 Sets a function governing the minimum alignment score needed for an alignment to
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1034 be considered "valid" (i.e. good enough to report). This is a function of read
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1035 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
1036 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
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1037 the default in `--local` mode is `G,20,8`.
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1038
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1039 -----
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1040
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1041 **Reporting options**::
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1042
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1043 -k <int>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1044 By default, `bowtie2` searches for distinct, valid alignments for each read.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1045 When it finds a valid alignment, it continues looking for alignments that are
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1046 nearly as good or better. The best alignment found is reported (randomly
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1047 selected from among best if tied). Information about the best alignments is
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1048 used to estimate mapping quality and to set SAM optional fields, such as
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1049 `AS:i` and `XS:i`.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1050
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1051 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1052 searches for at most `<int>` distinct, valid alignments for each read. The
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1053 search terminates when it can't find more distinct valid alignments, or when it
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1054 finds `<int>`, whichever happens first. All alignments found are reported in
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1055 descending order by alignment score. The alignment score for a paired-end
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1056 alignment equals the sum of the alignment scores of the individual mates. Each
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1057 reported read or pair alignment beyond the first has the SAM 'secondary' bit
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1058 (which equals 256) set in its FLAGS field. For reads that have more than
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1059 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1060 `<int>` alignments reported are the best possible in terms of alignment score.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1061 `-k` is mutually exclusive with `-a`.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1062
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1063 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1064 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1065
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1066 -a
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1067 Like `-k` but with no upper limit on number of alignments to search for. `-a`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1068 is mutually exclusive with `-k`.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1069
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1070 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1071 aligning reads to long, repetitive genomes this mode can be very, very slow.
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1072
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1073 -----
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1074
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1075 **Effort options**::
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1076
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1077 -D <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1078 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1079 moves on, using the alignments found so far. A seed extension "fails" if it
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1080 does not yield a new best or a new second-best alignment. This limit is
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1081 automatically adjusted up when -k or -a are specified. Default: 15.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1082
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1083 -R <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1084 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1085 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1086 (same length, same number of mismatches allowed) at different offsets and
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1087 searches for more alignments. A read is considered to have repetitive seeds if
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1088 the total number of seed hits divided by the number of seeds that aligned at
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1089 least once is greater than 300. Default: 2.
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1090
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1091 -----
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1092
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1093 **Paired-end options**::
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1094
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1095 -I/--minins <int>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1096 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1097 specified and a paired-end alignment consists of two 20-bp alignments in the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1098 appropriate orientation with a 20-bp gap between them, that alignment is
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1099 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1100 be valid in that case. If trimming options `-3` or `-5` are also used, the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1101 `-I` constraint is applied with respect to the untrimmed mates.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1102
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1103 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1104 run. This is because larger differences bewteen `-I` and `-X` require that
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1105 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1106 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1107 efficient.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1108
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1109 Default: 0 (essentially imposing no minimum)
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1110
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1111 -X/--maxins <int>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1112 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1113 is specified and a paired-end alignment consists of two 20-bp alignments in the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1114 proper orientation with a 60-bp gap between them, that alignment is considered
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1115 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1116 that case. If trimming options `-3` or `-5` are also used, the `-X`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1117 constraint is applied with respect to the untrimmed mates, not the trimmed
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1118 mates.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1119
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1120 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1121 run. This is because larger differences bewteen `-I` and `-X` require that
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1122 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1123 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1124 efficient.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1125
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1126 Default: 500.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1127
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1128 --fr/--rf/--ff
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1129 The upstream/downstream mate orientations for a valid paired-end alignment
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1130 against the forward reference strand. E.g., if `--fr` is specified and there is
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1131 a candidate paired-end alignment where mate 1 appears upstream of the reverse
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1132 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1133 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1134 complement of mate 1 and all other constraints are met, that too is valid.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1135 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1136 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1137 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1138 for Illumina's Paired-end Sequencing Assay).
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1139
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1140 --no-mixed
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1141 By default, when `bowtie2` cannot find a concordant or discordant alignment for
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1142 a pair, it then tries to find alignments for the individual mates. This option
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1143 disables that behavior.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1144
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1145 --no-discordant
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1146 By default, `bowtie2` looks for discordant alignments if it cannot find any
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1147 concordant alignments. A discordant alignment is an alignment where both mates
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1148 align uniquely, but that does not satisfy the paired-end constraints
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1149 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1150
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1151 --dovetail
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1152 If the mates "dovetail", that is if one mate alignment extends past the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1153 beginning of the other such that the wrong mate begins upstream, consider that
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
1154 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1155
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1156 --no-contain
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1157 If one mate alignment contains the other, consider that to be non-concordant.
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
1158 Default: a mate can contain the other in a concordant alignment.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1159
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1160 --no-overlap
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1161 If one mate alignment overlaps the other at all, consider that to be
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
1162 non-concordant. Default: mates can overlap in a concordant alignment.
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1163
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1164 ------
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1165
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1166 **SAM options**::
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1167
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1168 --rg-id <text>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1169 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1170 printed, with `<text>` as the value associated with the `ID:` tag. It also
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1171 causes the `RG:Z:` extra field to be attached to each SAM output record, with
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1172 value set to `<text>`.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1173
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1174 --rg <text>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1175 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1176 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
1177 must also be specified. This is because the `ID` tag is required by the SAM
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
1178 Specification. Specify `--rg` multiple times to set multiple fields. See the
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
1179 SAM Specification for details about what fields are legal.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1180
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1181 --omit-sec-seq
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1182 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1183 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1184 in those fields instead.
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1185
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1186 -----
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1187
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1188 **Other options**::
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1189
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1190 --reorder
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1191 Guarantees that output SAM records are printed in an order corresponding to the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1192 order of the reads in the original input file, even when `-p` is set greater
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1193 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1194 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1195 not specified. Has no effect if `-p` is set to 1, since output order will
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1196 naturally correspond to input order in that case.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1197
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1198 --seed <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1199 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1200
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1201 --non-deterministic
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1202 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1203 seeds the generator with a number derived from (a) the read name, (b) the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1204 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1205 option. This means that if two reads are identical (same name, same
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1206 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1207 for both, even if there was ambiguity. When `--non-deterministic` is specified,
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1208 Bowtie 2 re-initializes its pseudo-random generator for each read using the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1209 current time. This means that Bowtie 2 will not necessarily report the same
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1210 alignment for two identical reads. This is counter-intuitive for some users,
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1211 but might be more appropriate in situations where the input consists of many
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1212 identical reads.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1213
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1214 -----
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1215
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1216
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1217 **Paired-end (and mate-pair) data in fastq format**
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1218
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1219 Paired end datasets can be represented as two individual datasets:
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1220
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1221 First dataset::
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1222
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1223 @1/1
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1224 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1225 +
7e0b333f39e1 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
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1227 @2/1
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1228 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1229 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1230 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1231
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1232 Second dataset::
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1233
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1234 @1/2
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1235 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1236 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1237 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1238 @2/2
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1239 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1240 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1241 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1242
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1243 Or a single *interleaved* dataset::
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1244
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1245 @1/1
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1246 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1247 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1248 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1249 @1/2
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1250 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1251 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1252 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1253 @2/1
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1254 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1255 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1256 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1257 @2/2
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1258 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1259 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1260 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1261 ]]></help>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1262 <citations>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
1263 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
1264 <citation type="doi">10.1038/nmeth.1923</citation>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
1265 </citations>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1266 </tool>