Mercurial > repos > devteam > bowtie2

annotate bowtie2_wrapper.xml @ 18:e0ca9500999b 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 a887e11c533af3ed3734c26da2da33aa8acbbce9
author iuc
date Fri, 24 Nov 2017 07:43:48 -0500
parents 69f044db2445
children 7f9d1892eb1b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
1 <tool id="bowtie2" name="Bowtie2" version="2.3.3.1" profile="17.01">
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>
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
7 <requirement type="package" version="2.3.3.1">bowtie2</requirement>
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
8 <requirement type="package" version="1.6">samtools</requirement>
11
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[
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
12 ## prepare bowtie2 index
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
13 #set index_path = ''
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
14 #if str($reference_genome.source) == "history":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
15 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome &&
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
16 ln -s -f '$reference_genome.own_file' genome.fa &&
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
17 #set index_path = 'genome'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
18 #else:
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 = $reference_genome.index.fields.path
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
20 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
21
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
22 ## Link in the input files, so bowtie2 can tell their type
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
23
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
24 #set compressed="False"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
25 #set reads_are_fastq = True
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
26 #if str($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
27 #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
28 #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
29 #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
30 #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
31 #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
32 #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
33 #else if $library.input_1.is_of_type('fasta'):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
34 #set reads_are_fastq = False
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
35 #set read1 = "input_f.fasta"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
36 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
37 #set read1 = "input_f.fastq"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
38 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
39 ln -f -s '${library.input_1}' ${read1} &&
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
40
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
41 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
42 #set read2 = "input_r.fastq.gz"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
43 #set compressed = "GZ"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
44 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
45 #set read2 = "input_r.fastq.bz2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
46 #set compressed = "BZ2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
47 #else if $library.input_2.is_of_type('fasta'):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
48 #set read2 = "input_r.fasta"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
49 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
50 #set read2 = "input_r.fastq"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
51 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
52 ln -f -s '${library.input_2}' ${read2} &&
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
53 #else if str($library.type) == 'paired_collection':
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
54 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
55 #set read1 = "input_f.fastq.gz"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
56 #set compressed = "GZ"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
57 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
58 #set read1 = "input_f.fastq.bz2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
59 #set compressed = "BZ2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
60 #else if $library.input_1.forward.is_of_type('fasta'):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
61 #set reads_are_fastq = False
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
62 #set read1 = "input_f.fasta"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
63 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
64 #set read1 = "input_f.fastq"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
65 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
66 ln -s '${library.input_1.forward}' ${read1} &&
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
67
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
68 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
69 #set read2 = "input_r.fastq.gz"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
70 #set compressed = "GZ"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
71 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
72 #set read2 = "input_r.fastq.bz2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
73 #set compressed = "BZ2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
74 #else if $library.input_1.reverse.is_of_type("fasta"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
75 #set read2 = "input_r.fasta"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
76 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
77 #set read2 = "input_r.fastq"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
78 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
79 ln -s '${library.input_1.reverse}' ${read2} &&
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
80
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
81 #else if str($library.type) == 'paired_interleaved':
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
82 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
83 #set read1 = "input_il.fastq.gz"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
84 #set compressed = "GZ"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
85 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
86 #set read1 = "input_il.fastq.bz2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
87 #set compressed = "BZ2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
88 #else if $library.input_1.is_of_type("fasta"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
89 #set reads_are_fastq = False
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
90 #set read1 = "input_il.fasta"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
91 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
92 #set read1 = "input_il.fastq"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
93 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
94 ln -s '${library.input_1}' ${read1} &&
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
95 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
96 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
97 #set read1 = "input_f.fastq.gz"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
98 #set compressed = "GZ"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
99 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
100 #set read1 = "input_f.fastq.bz2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
101 #set compressed = "BZ2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
102 #else if $library.input_1.is_of_type("fasta"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
103 #set reads_are_fastq = False
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
104 #set read1 = "input_f.fasta"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
105 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
106 #set read1 = "input_f.fastq"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
107 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
108 ln -s '${library.input_1}' ${read1} &&
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
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
111 ## execute bowtie2
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 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 ## 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
116 -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
117
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
118 ## index file path
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
119 -x '$index_path'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
120
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
121 ## Input reads are fasta?
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
122 #if not reads_are_fastq:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
123 -f
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
124 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
125
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
126 ## Input reads
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
127 #if str( $library.type ) == "single":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
128 -U '${read1}'
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.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
130 #if $compressed == "GZ":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
131 --un-gz '${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
132 #else if $compressed == "BZ2":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
133 --un-bz2 '${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
134 #else:
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
135 --un '${output_unaligned_reads_l}'
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
136 #end if
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
137 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
138 #if str( $library.aligned_file ) == "true":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
139 #if $compressed == "GZ":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
140 --al-gz '${output_aligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
141 #else if $compressed == "BZ2":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
142 --al-bz2 '${output_aligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
143 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
144 --al '${output_aligned_reads_l}'
16
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
145 #end if
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
146 #end if
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
147
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
148 #elif str( $library.type ) == "paired_interleaved":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
149 --interleaved '${read1}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
150 #if str( $library.unaligned_file ) == "true":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
151 #if $compressed == "GZ":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
152 --un-gz '${output_unaligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
153 #else if $compressed == "BZ2":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
154 --un-bz2 '${output_unaligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
155 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
156 --un '${output_unaligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
157 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
158 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
159 #if str( $library.aligned_file ) == "true":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
160 #if $compressed == "GZ":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
161 --al-gz '${output_aligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
162 #else if $compressed == "BZ2":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
163 --al-bz2 '${output_aligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
164 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
165 --al '${output_aligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
166 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
167 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
168 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
169 -1 '${read1}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
170 -2 '${read2}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
171 #if str( $library.unaligned_file ) == "true":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
172 #if $compressed == "GZ":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
173 --un-conc-gz '${output_unaligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
174 #else if $compressed == "BZ2":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
175 --un-conc-bz2 '${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
176 #else:
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 '${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 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
179 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
180 #if str( $library.aligned_file ) == "true":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
181 #if $compressed == "GZ":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
182 --al-conc-gz '${output_aligned_reads_l}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
183 #else if $compressed == "BZ2":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
184 --al-conc-bz2 '${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
185 #else:
18
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 '${output_aligned_reads_l}'
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
187 #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
188 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
189 #if str( $library.paired_options.paired_options_selector ) == "yes":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
190 -I ${library.paired_options.I}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
191 -X ${library.paired_options.X}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
192 ${library.paired_options.fr_rf_ff}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
193 ${library.paired_options.no_mixed}
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.no_discordant}
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.dovetail}
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_contain}
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.no_overlap}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
198 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
199 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
200
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
201 ## Read group information.
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
202 @define_read_group_helpers@
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
203 #if str( $library.type ) == "single":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
204 #set $rg_auto_name = $read_group_name_default($library.input_1)
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
205 #elif str( $library.type ) == "paired":
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, $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
207 #else
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)
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
209 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
210 @set_use_rg_var@
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
211 @set_read_group_vars@
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
212 #if $use_rg
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
213 $format_read_group("", $rg_id, '"', arg='--rg-id ')
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
214 $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
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("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
216 $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
217 $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
218 $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
219 $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
220 $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
221 $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
222 $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
223 $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
224 $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
225 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
226
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
227 ## Analysis type
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
228 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
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.presets
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
230 #elif str( $analysis_type.analysis_type_selector ) == "full":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
231 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
232 --skip ${analysis_type.input_options.skip}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
233 --qupto ${analysis_type.input_options.qupto}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
234 --trim5 ${analysis_type.input_options.trim5}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
235 --trim3 ${analysis_type.input_options.trim3}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
236 ${analysis_type.input_options.qv_encoding}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
237 ${analysis_type.input_options.solexa_quals}
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.int_quals}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
239 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
240
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
241 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
242 -N ${analysis_type.alignment_options.N}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
243 -L ${analysis_type.alignment_options.L}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
244 -i '${analysis_type.alignment_options.i}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
245 --n-ceil '${analysis_type.alignment_options.n_ceil}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
246 --dpad ${analysis_type.alignment_options.dpad}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
247 --gbar ${analysis_type.alignment_options.gbar}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
248 ${analysis_type.alignment_options.ignore_quals}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
249 ${analysis_type.alignment_options.nofw}
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.norc}
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.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
252 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
253 --end-to-end
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
254 --score-min '${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
255 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
256 --local
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
257 --score-min '${analysis_type.alignment_options.align_mode.score_min_loc}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
258 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
259 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
260
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
261 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
262 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
263 --ma ${analysis_type.scoring_options.ma}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
264 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
265 --mp '${analysis_type.scoring_options.mp}'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
266 --np ${analysis_type.scoring_options.np}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
267 --rdg ${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
268 --rfg ${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
269 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
270
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
271 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
272 -k ${analysis_type.reporting_options.k}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
273 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
274 -a
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
275 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
276
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
277 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
278 -D ${analysis_type.effort_options.D}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
279 -R ${analysis_type.effort_options.R}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
280 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
281
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
282 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
283 ${analysis_type.sam_options.no_unal}
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.sam_options.omit_sec_seq}
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.sam_options.sam-no-qname-trunc}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
286 ${analysis_type.sam_options.xeq}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
287 ${analysis_type.sam_options.soft-clipped-unmapped-tlen}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
288 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
289
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
290 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
291 ${analysis_type.other_options.reorder}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
292 ${analysis_type.other_options.non_deterministic}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
293 --seed ${analysis_type.other_options.seed}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
294 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
295
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
296 #elif str( $analysis_type.analysis_type_selector ) == "cline":
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
297 ${analysis_type.cline}
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
298 #end if
10
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
299
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
300 ## mapping stats (i.e. stderr from bowtie2)
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
301 #if $save_mapping_stats
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
302 2> '$mapping_stats'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
303 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
304
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
305 ## output file
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
306 #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
307 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
308 #else
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
309 > '$output_sam'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
310 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
311
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
312 ## rename unaligned sequence files
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
313 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
314 #from os.path import splitext
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
315 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
316 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
317 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
318 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
319 #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
320 #from os.path import splitext
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
321 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
322 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
323 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
324 #end if
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
325
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
326 ]]></command>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
327 <inputs>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
328 <!-- single/paired -->
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
329 <conditional name="library">
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
330 <param name="type" type="select" label="Is this single or paired library">
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
331 <option value="single">Single-end</option>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
332 <option value="paired">Paired-end</option>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
333 <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
334 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
335 </param>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
336
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
337 <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
338 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
339 <expand macro="align_unalign" />
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
340 </when>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
341 <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
342 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #1" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
343 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #2" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
344 <expand macro="align_unalign" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
345 <expand macro="paired_end_options" />
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
346 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
347 <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
348 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
15
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="align_unalign" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
350 <expand macro="paired_end_options" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
351 </when>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
352 <when value="paired_interleaved">
16
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
353 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTQ file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;. --interleaved"/>
15
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="align_unalign" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
355 <expand macro="paired_end_options" />
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
356 </when>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
357 </conditional>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
358 <!-- reference genome -->
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
359 <conditional name="reference_genome">
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
360 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
361 <option value="indexed">Use a built-in genome index</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
362 <option value="history">Use a genome from the history and build index</option>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
363 </param>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
364 <when value="indexed">
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
365 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
366 <options from_data_table="bowtie2_indexes">
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
367 <filter type="sort_by" column="2"/>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
368 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
369 </options>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
370 </param>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
371 </when>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
372 <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
373 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
374 </when>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
375 </conditional>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
376 <!-- read group settings -->
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
377 <expand macro="read_group_conditional" />
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
378 <conditional name="analysis_type">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
379 <param name="analysis_type_selector" type="select" label="Select analysis mode">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
380 <option value="simple">1: Default setting only</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
381 <option value="full">2: Full parameter list</option>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
382 </param>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
383 <when value="simple">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
384 <param name="presets" type="select" display="radio" label="Do you want to use presets?" help="Allow selecting among several preset parameter settings. Choosing between these will result in dramatic changes in runtime. See help below to understand effects of these presets.">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
385 <option value="no_presets" selected="True">No, just use defaults</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
386 <option value="--very-fast">Very fast end-to-end (--very-fast)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
387 <option value="--fast">Fast end-to-end (--fast)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
388 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
389 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
390 <option value="--very-fast-local">Very fast local (--very-fast-local)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
391 <option value="--fast-local">Fast local (--fast-local)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
392 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
393 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
394 </param>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
395 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
396 <when value="full">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
397 <conditional name="input_options">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
398 <param name="input_options_selector" type="select" label="Do you want to tweak input options?" help="See &quot;Input Options&quot; section of Help below for information">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
399 <option value="yes">Yes</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
400 <option value="no" selected="true">No</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
401 </param>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
402 <when value="yes">
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
403 <param name="skip" type="integer" min="0" value="0" label="Skip (i.e. do not align) the first that many reads or pairs in the input" help="-s/--skip; default=0"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
404 <param name="qupto" type="integer" min="1" value="100000000" label="Align the first that many reads or read pairs from the input (after the -s/--skip reads or pairs have been skipped), then stop" help="-u/--qupto; for default behavior (no limit) leave this value very large"/>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
405 <param name="trim5" type="integer" min="0" value="0" label="Trim that many bases from 5' (left) end of each read before alignment" help="-5/--trim5; default=0"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
406 <param name="trim3" type="integer" min="0" value="0" label="Trim that many bases from 3' (right) end of each read before alignment" help="-3/--trim3; default=0"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
407 <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
408 <option value="--phred33" selected="True">Input qualities are ASCII chars equal to the Phred quality plus 33. This is also called the "Phred+33" encoding, which is used by the very latest Illumina pipelines (--phred33)</option>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
409 <option value="--phred64">Input qualities are ASCII chars equal to the Phred quality plus 64. This is also called the "Phred+64" encoding (--phred64)</option>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
410 </param>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
411 <param name="solexa_quals" type="boolean" truevalue="--solexa-quals" falsevalue="" checked="False" label="Convert input qualities from Solexa (which can be negative) to Phred (which can't). This scheme was used in older Illumina GA Pipeline versions (prior to 1.3)" help="--solexa-quals; default=False"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
412 <param name="int_quals" type="boolean" truevalue="--int-quals" falsevalue="" checked="False" label="Quality values are represented in the read input file as space-separated ASCII integers, e.g., 40 40 30 40..., rather than ASCII characters, e.g., II?I.... Integers are treated as being on the Phred quality scale unless --solexa-quals is also specified" help="--int-quals; default=False"/>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
413 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
414 <when value="no">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
415 <!-- do nothing -->
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
416 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
417 </conditional>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
418 <conditional name="alignment_options">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
419 <param name="alignment_options_selector" type="select" label="Do you want to tweak alignment options?" help="See &quot;Alignment Options&quot; section of Help below for information">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
420 <option value="yes">Yes</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
421 <option value="no" selected="true">No</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
422 </param>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
423 <when value="yes">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
424 <param name="N" type="integer" min="0" max="1" value="0" label="Set the number of mismatches to be allowed in a seed alignment during multiseed alignment (see `Multiseed alignment` section of help below)" help="-N; Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity; default=0"/>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
425 <param name="L" type="integer" min="0" max="32" value="22" label="Sets the length of the seed substrings to align during multiseed alignment (see `Multiseed alignment` section of help below)" help="-L; Smaller values make alignment slower but more sensitive. Default=22"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
426 <param name="i" type="text" value="S,1,1.15" label="Set a function governing the interval between seed substrings to use during multiseed alignment (see `Multiseed alignment` section of help below). Also see description of this option below in the help section" help="-i; Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. If the function returns a result less than 1, it is rounded up to 1. Default=`S,1,1.15`"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
427 <param name="n_ceil" type="text" value="L,0,0.15" label="Set a function governing the maximum number of ambiguous characters (usually `N`s and/or `.`s) allowed in a read as a function of read length" help="--n-ceil; For instance, specifying `L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, where x is the read length. Reads exceeding this ceiling are filtered out. Default=`L,0,0.15`"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
428 <param name="dpad" type="integer" min="0" value="15" label="Pad dynamic programming problems by that many columns on either side to allow gaps" help="--dpad; default=15"/>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
429 <param name="gbar" type="integer" min="0" value="4" label="Disallow gaps within that many positions of the beginning or end of the read" help="--gbar; default=4"/>
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
430 <param name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" label="When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value" help="--ignore-quals; input is treated as though all quality values are high; default=False"/>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
431 <param name="nofw" type="boolean" truevalue="--nofw" falsevalue="" label="Do not attempt to align unpaired reads to the forward (Watson) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
432 <param name="norc" type="boolean" truevalue="--norc" falsevalue="" label="Do not attempt to align unpaired reads to the reverse (Crick) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
433 <param name="no_1mm_upfront" type="boolean" truevalue="--no-1mm-upfront" falsevalue="" label="Prevent searching for 1-mismatch end-to-end alignments before using the multiseed heuristic (see `Multiseed alignment` section of help below)" help="--no-1mm-upfront; By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch end-to-end alignment for the read *before* trying the multiseed heuristic. Such alignments can be found very quickly, and many short read alignments have exact or near-exact end-to-end alignments. However, this can lead to unexpected alignments when the user also sets options governing the multiseed heuristic, like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal to the length of the read, the user will be surprised to find 1-mismatch alignments reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end alignments before using the multiseed heuristic, which leads to the expected behavior when combined with options such as `-L` and `-N`. This comes at the expense of speed; Default=False"/>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
434 <conditional name="align_mode">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
435 <param name="align_mode_selector" type="select" display="radio" label="Select between `--local` and `--end-to-end` alignment modes" help="--local and --end-to-end; see help below for detailed explanation; default=--end-to-end">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
436 <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
437 <option value="local">Local (--local)</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
438 </param>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
439 <when value="end-to-end">
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
440 <param name="score_min_ete" type="text" value="L,-0.6,-0.6" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
441 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
442 <when value="local">
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
443 <param name="score_min_loc" type="text" value="G,20,8" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
444 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
445 </conditional>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
446 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
447 <when value="no">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
448 <!-- do nothing -->
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
449 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
450 </conditional>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
451 <conditional name="scoring_options">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
452 <param name="scoring_options_selector" type="select" label="Do you want to tweak scoring options?" help="See &quot;Scoring Options&quot; section of Help below for information">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
453 <option value="yes">Yes</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
454 <option value="no" selected="true">No</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
455 </param>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
456 <when value="yes">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
457 <param name="ma" type="integer" value="2" label="Set the match bonus" help="--ma; In `--local` mode match bonus is added to the alignment score for each position where a read character aligns to a reference character and the characters match. Not used in `--end-to-end` mode; Default=2"/>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
458 <param name="mp" type="text" value="6,2" label="Set the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers" help="--mp; A number less than or equal to `MX` and greater than or equal to `MN` is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`. Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` where Q is the Phred quality value; Default=6,2"/>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
459 <param name="np" type="integer" value="1" label="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as `N`" help="--np; Default=1"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
460 <param name="rdg_read_open" type="integer" value="5" label="Set the read gap opening penalty" help="--rdg; this is the first component of --rdg flag - opening penalty; Default=5"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
461 <param name="rdg_read_extend" type="integer" value="3" label="Set the read gap extension penalty" help="--rdg; this is the second component of --rdg flag - extension penalty; Default=3"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
462 <param name="rfg_ref_open" type="integer" value="5" label="Set the reference gap opening penalty" help="--rfg; this is the first component of --rfg flag - opening penalty; Default=5"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
463 <param name="rfg_ref_extend" type="integer" value="3" label="Set the reference gap extension penalty" help="--rfg; this is the second component of --rfg flag - extension penalty; Default=3"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
464 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
465 <when value="no">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
466 <!-- do nothing -->
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
467 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
468 </conditional>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
469 <conditional name="reporting_options">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
470 <param name="reporting_options_selector" type="select" label="Do you want to use -a or -k options" help="Make sure you understand implications of setting -k and -a. See &quot;Reporting Options&quot; section of Help below for information on -k and -a options">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
471 <option value="no" selected="true">No, do not set</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
472 <option value="k">Set -k option and enter -k value</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
473 <option value="a">Set -a option</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
474 </param>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
475 <when value="no">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
476 <!-- do nothing -->
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
477 </when>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
478 <when value="k">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
479 <param name="k" type="integer" min="1" value="1" label="Searches for at most that many distinct, valid alignments for each read" help="-k; see detailed description of this option in the help section below. Note: Bowtie 2 is not designed with large values for `-k` in mind, and when aligning reads to long, repetitive genomes large `-k` can be very, very slow"/>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
480 </when>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
481 <when value="a">
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
482 <!-- do nothing here; set -a flag on the command line-->
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
483 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
484 </conditional>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
485 <conditional name="effort_options">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
486 <param name="effort_options_selector" type="select" label="Do you want to tweak effort options?" help="See &quot;Effort Options&quot; section of Help below for information">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
487 <option value="yes">Yes</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
488 <option value="no" selected="true">No</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
489 </param>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
490 <when value="yes">
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
491 <param name="D" type="integer" value="15" min="0" label="Attempt that many consecutive seed extension attempts to `fail` before Bowtie 2 moves on, using the alignments found so far" help="-D; A seed extension `fails` if it does not yield a new best or a new second-best alignment. This limit is automatically adjusted up when -k or -a are specified. Default=15"/>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
492 <param name="R" type="integer" value="2" min="0" label="Set the maximum number of times Bowtie 2 will `re-seed` reads with repetitive seeds" help="When `re-seeding`, Bowtie 2 simply chooses a new set of reads (same length, same number of mismatches allowed) at different offsets and searches for more alignments. A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than 300. Default=2"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
493 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
494 <when value="no">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
495 <!-- do nothing -->
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
496 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
497 </conditional>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
498 <conditional name="sam_options">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
499 <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See &quot;Output Options&quot; section of Help below for information">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
500 <option value="yes">Yes</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
501 <option value="no" selected="true">No</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
502 </param>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
503 <when value="yes">
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
504 <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
505 <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
18
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
506 <param 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"/>
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
507 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
iuc
parents: 17
diff changeset
508 <param argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
509 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
510 <when value="no">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
511 <!-- do nothing -->
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
512 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
513 </conditional>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
514 <conditional name="other_options">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
515 <param name="other_options_selector" type="select" label="Do you want to tweak Other Options?" help="See &quot;Other Options&quot; section of Help below for information">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
516 <option value="yes">Yes</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
517 <option value="no" selected="true">No</option>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
518 </param>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
519 <when value="yes">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
520 <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" label="Guarantee that output SAM records are printed in an order corresponding to the order of the reads in the original input file" help="--reorder; Default=False"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
521 <param name="seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="--seed; Default=0"/>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
522 <param name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="--non-deterministic; see Help below for explanation of this option; default=False"/>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
523 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
524 <when value="no">
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
525 <!-- do nothing -->
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
526 </when>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
527 </conditional>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
528 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
529 </when>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
530 </conditional>
10
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
531 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
532 </inputs>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
533 <!-- define outputs -->
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
534 <outputs>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
535 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
536 <filter>library['unaligned_file'] is True</filter>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
537 <actions>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
538 <conditional name="library.type">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
539 <when value="single">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
540 <action type="format">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
541 <option type="from_param" name="library.input_1" param_attribute="ext" />
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
542 </action>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
543 </when>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
544 <when value="paired">
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_collection">
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="forward.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 </conditional>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
555 </actions>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
556 </data>
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
557 <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
558 <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
559 <actions>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
560 <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
561 <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
562 <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
563 <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
564 </action>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
565 </when>
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="paired">
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_collection">
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="forward.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 </conditional>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
577 </actions>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
578 </data>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
579 <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
580 <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
581 <actions>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
582 <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
583 <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
584 <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
585 <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
586 </action>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
587 </when>
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_collection">
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_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
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 </conditional>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
594 </actions>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
595 </data>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
596 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
597 <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
598 <actions>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
599 <conditional name="library.type">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
600 <when value="paired">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
601 <action type="format">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
602 <option type="from_param" name="library.input_2" param_attribute="ext" />
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
603 </action>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
604 </when>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
605 <when value="paired_collection">
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_1" param_attribute="reverse.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 </conditional>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
611 </actions>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
612 </data>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
613 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
614 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
615 <actions>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
616 <conditional name="reference_genome.source">
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
617 <when value="indexed">
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
618 <action type="metadata" name="dbkey">
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
619 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
620 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
621 <filter type="param_value" ref="reference_genome.index" column="0"/>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
622 </option>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
623 </action>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
624 </when>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
625 <when value="history">
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_param" name="reference_genome.own_file" param_attribute="dbkey" />
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
628 </action>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
629 </when>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
630 </conditional>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
631 </actions>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
632 </data>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
633 <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
634 <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
635 <actions>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
636 <conditional name="reference_genome.source">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
637 <when value="indexed">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
638 <action type="metadata" name="dbkey">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
639 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
640 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
641 <filter type="param_value" ref="reference_genome.index" column="0"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
642 </option>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
643 </action>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
644 </when>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
645 <when value="history">
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_param" name="reference_genome.own_file" param_attribute="dbkey" />
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
648 </action>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
649 </when>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
650 </conditional>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
651 </actions>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
652 </data>
10
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
653 <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
654 <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
655 </data>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
656 </outputs>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
657 <tests>
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
658 <test>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
659 <!-- test on paired-end datasets -->
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
660 <param name="type" value="paired"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
661 <param name="paired_options_selector" value="no"/>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
662 <param name="unaligned_file" value="false"/>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
663 <param name="analysis_type_selector" value="simple"/>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
664 <param name="source" value="history" />
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
665 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
666 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
667 <param name="own_file" value="bowtie2-ref.fasta" />
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
668 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
669 </test>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
670 <test>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
671 <!-- test on paired collection -->
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
672 <param name="type" value="paired_collection"/>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
673 <param name="paired_options_selector" value="no"/>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
674 <param name="unaligned_file" value="false"/>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
675 <param name="analysis_type_selector" value="simple"/>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
676 <param name="source" value="history" />
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
677 <param name="input_1">
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
678 <collection type="paired">
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
679 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" />
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
680 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" />
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
681 </collection>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
682 </param>
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="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
684 <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
685 </test>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
686 <test>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
687 <!-- test on paired-end datasets with read group info -->
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
688 <param name="type" value="paired"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
689 <param name="paired_options_selector" value="no"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
690 <param name="unaligned_file" value="false"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
691 <param name="analysis_type_selector" value="simple"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
692 <param name="rg_selector" value="set"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
693 <param name="ID" value="rg1"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
694 <param name="PL" value="CAPILLARY"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
695 <param name="source" value="history" />
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
696 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
697 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
698 <param name="own_file" value="bowtie2-ref.fasta" />
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
699 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
700 </test>
10
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
701 <test>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
702 <!-- test on paired-end datasets with stats output -->
10
fed480fea9f0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents: 8
diff changeset
703 <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
704 <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
705 <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
706 <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
707 <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
708 <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
709 <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
710 <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
711 <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
712 <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
713 <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
714 <assert_contents>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
715 <has_text text="of these" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
716 </assert_contents>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
717 </output>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
718 </test>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
719 <test>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
720 <!-- test on interleaved dataset -->
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
721 <param name="type" value="paired_interleaved"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
722 <!-- <param name="paired_options_selector" value="no"/> -->
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
723 <param name="unaligned_file" value="false"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
724 <param name="analysis_type_selector" value="simple"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
725 <param name="rg_selector" value="set"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
726 <param name="ID" value="rg1"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
727 <param name="PL" value="CAPILLARY"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
728 <param name="source" value="history" />
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="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
730 <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
731 <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
732 </test>
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
733 <test>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
734 <!-- test on fastqsanger.gz paired-end datasets -->
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
735 <param name="type" value="paired"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
736 <param name="paired_options_selector" value="no"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
737 <param name="unaligned_file" value="false"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
738 <param name="analysis_type_selector" value="simple"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
739 <param name="source" value="history" />
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
740 <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
741 <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
742 <param name="own_file" value="bowtie2-ref.fasta" />
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
743 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
744 </test>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
devteam
parents: 13
diff changeset
745 <test>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
746 <!-- test on fastqsanger.bz2 paired-end datasets -->
14
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="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
748 <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
749 <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
750 <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
751 <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
752 <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
753 <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
754 <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
755 <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
756 </test>
16
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
757 <test>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
758 <!-- test on fasta paired-end datasets -->
16
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
759 <param name="type" value="paired"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
760 <param name="paired_options_selector" value="no"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
761 <param name="unaligned_file" value="false"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
762 <param name="analysis_type_selector" value="simple"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
763 <param name="source" value="history" />
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
764 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
765 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
766 <param name="own_file" value="bowtie2-ref.fasta" />
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
767 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
def46fdb3909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 5581ee25e468d4a1144ce6e5e511cb29cd51cf1f
iuc
parents: 15
diff changeset
768 </test>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
769 </tests>
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
770 <help><![CDATA[
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
771 **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
772
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
773 Bowtie2_ is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 supports gapped, local, and paired-end alignment modes. Galaxy wrapper for Bowtie 2 outputs alignments in `BAM format`_, enabling interoperation with a large number of other tools available at this site.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
774 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
775
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
776 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
777 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
778 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
779
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
780 -----
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
781
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
782 **Selecting reference genomes for Bowtie2**
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
783
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
784 Galaxy wrapper for Bowtie2 allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
785
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
786 1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bowtie2-build utility and are ready to be mapped against.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
787 2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome from this dropdown will cause Galaxy to first transparently index it using bowtie2-build command, and then run mapping with bowtie2.
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
788
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
789 If your genome of interest is not listed here you have two choices:
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
790
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
791 1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
792 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
793
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
794 ------
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
795
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
796 .. class:: infomark
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
797
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
798 **Bowtie2 options**
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
799
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
800 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
801
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
802 -----
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
803
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
804 **Inputs**
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
805
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
806 Bowtie 2 accepts files in Sanger FASTQ format (single or paired-end). Paired-end data can represented as two individual (forward and reverse) datasets, as well as a single interleaved dataset (see an example at the end of the help section).
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
807
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
808 ------
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
809
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
810 **Input options**::
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
811
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
812 --interleaved
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
813 Reads interleaved FASTQ files where the first two records (8 lines) represent a mate pair.
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
814
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
815 -s/--skip <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
816 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
817
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
818 -u/--qupto <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
819 Align the first `<int>` reads or read pairs from the input (after the
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
820 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
821
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
822 -5/--trim5 <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
823 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
824
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
825 -3/--trim3 <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
826 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
827
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
828 --phred33
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
829 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
830 also called the "Phred+33" encoding, which is used by the very latest Illumina
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
831 pipelines.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
832
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
833 --phred64
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
834 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
835 also called the "Phred+64" encoding.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
836
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
837 --solexa-quals
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
838 Convert input qualities from Solexa Phred quality (which can be negative) to
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
839 Phred Phred quality (which can't). This scheme was used in older Illumina GA
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
840 Pipeline versions (prior to 1.3). Default: off.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
841
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
842 --int-quals
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
843 Quality values are represented in the read input file as space-separated ASCII integers, e.g., `40 40 30 40`..., rather than ASCII characters, e.g., `II?I`....
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
844 Integers are treated as being on the Phred quality scale unless
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
845 `--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
846
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
847 ------
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
848
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
849 **Presets in `--end-to-end` mode**::
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
850
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
851 --very-fast
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
852 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
853
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
854 --fast
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
855 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
856
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
857 --sensitive
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
858 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
859
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
860 --very-sensitive
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
861 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
862
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
863 ------
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
864
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
865 **Presets options in `--local` mode**::
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
866
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
867 --very-fast-local
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
868 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
869
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
870 --fast-local
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
871 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
872
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
873 --sensitive-local
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
874 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
875
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
876 --very-sensitive-local
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
877 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
878
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
879 ------
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
880
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
881 **Alignment options**::
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
882
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
883 -N <int>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
884 Sets the number of mismatches to allowed in a seed alignment during multiseed
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
885 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
886 (often much slower) but increases sensitivity. Default: 0.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
887
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
888 -L <int>
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
889 Sets the length of the seed substrings to align during multiseed alignment.
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
890 Smaller values make alignment slower but more sensitive. Default: the
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
891 `--sensitive` preset is used by default, which sets `-L` to 22 in
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
892 `--end-to-end` mode and to 20 in `--local` mode.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
893
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
894 -i <func>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
895 Sets a function governing the interval between seed substrings to use during
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
896 multiseed alignment. For instance, if the read has 30 characers, and seed
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
897 length is 10, and the seed interval is 6, the seeds extracted will be:
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
898
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
899 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
900 Seed 1 fw: TAGCTACGCT
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
901 Seed 1 rc: AGCGTAGCTA
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
902 Seed 2 fw: CGCTCTACGC
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
903 Seed 2 rc: GCGTAGAGCG
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
904 Seed 3 fw: ACGCTATCAT
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
905 Seed 3 rc: ATGATAGCGT
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
906 Seed 4 fw: TCATGCATAA
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
907 Seed 4 rc: TTATGCATGA
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
908
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
909 Since it's best to use longer intervals for longer reads, this parameter sets
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
910 the interval as a function of the read length, rather than a single
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
911 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
912 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
913 If the function returns a result less than
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
914 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
915 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
916 in `--local` mode.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
917
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
918 --n-ceil <func>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
919 Sets a function governing the maximum number of ambiguous characters (usually
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
920 `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
921 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
922 where x is the read length. Reads exceeding this ceiling are filtered out.
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
923 Default: `L,0,0.15`.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
924
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
925 --dpad <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
926 "Pads" dynamic programming problems by `<int>` columns on either side to allow
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
927 gaps. Default: 15.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
928
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
929 --gbar <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
930 Disallow gaps within `<int>` positions of the beginning or end of the read.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
931 Default: 4.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
932
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
933 --ignore-quals
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
934 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
935 mismatched position to be the highest possible, regardless of the actual value.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
936 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
937 default behavior when the input doesn't specify quality values (e.g. in `-f`,
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
938 `-r`, or `-c` modes).
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
939
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
940 --nofw/--norc
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
941 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
942 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
943 not attempt to align unpaired reads against the reverse-complement (Crick)
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
944 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
945 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
946 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
947 (Crick) strand. Default: both strands enabled.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
948
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
949 --no-1mm-upfront
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
950 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
951 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
952 alignments can be found very quickly, and many short read alignments have exact or
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
953 near-exact end-to-end alignments. However, this can lead to unexpected
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
954 alignments when the user also sets options governing the multiseed heuristic,
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
955 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
956 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
957 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
958 alignments before using the multiseed heuristic, which leads to the expected
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
959 behavior when combined with options such as `-L` and `-N`. This comes at the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
960 expense of speed.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
961
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
962 --end-to-end
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
963 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
964 other, without any trimming (or "soft clipping") of characters from either end.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
965 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
966 are less than or equal to 0, and the greatest possible alignment score is 0.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
967 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
968
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
969 --local
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
970 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
971 to the other. Rather, some characters may be omitted ("soft clipped") from the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
972 ends in order to achieve the greatest possible alignment score. The match bonus
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
973 `--ma` is used in this mode, and the best possible alignment score is equal to
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
974 the match bonus (`--ma`) times the length of the read. Specifying `--local`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
975 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
976 the local version of the preset (`--very-fast-local`). This is mutually
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
977 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
978
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
979 -----
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
980
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
981 **Scoring options**::
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
982
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
983 --ma <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
984 Sets the match bonus. In `--local` mode `<int>` is added to the alignment
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
985 score for each position where a read character aligns to a reference character
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
986 and the characters match. Not used in `--end-to-end` mode. Default: 2.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
987
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
988 --mp MX,MN
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
989 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
990 number less than or equal to `MX` and greater than or equal to `MN` is
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
991 subtracted from the alignment score for each position where a read character
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
992 aligns to a reference character, the characters do not match, and neither is an
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
993 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
994 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
995 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
996
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
997 --np <int>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
998 Sets penalty for positions where the read, reference, or both, contain an
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
999 ambiguous character such as `N`. Default: 1.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1000
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1001 --rdg <int1>,<int2>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1002 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1003 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
2
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 --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
1006 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
1007 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1008 5, 3.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1009
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1010 --score-min <func>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1011 Sets a function governing the minimum alignment score needed for an alignment to
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1012 be considered "valid" (i.e. good enough to report). This is a function of read
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1013 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
1014 to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1015 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
1016
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1017 -----
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1018
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1019 **Reporting options**::
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1020
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1021 -k <int>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1022 By default, `bowtie2` searches for distinct, valid alignments for each read.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1023 When it finds a valid alignment, it continues looking for alignments that are
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1024 nearly as good or better. The best alignment found is reported (randomly
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1025 selected from among best if tied). Information about the best alignments is
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1026 used to estimate mapping quality and to set SAM optional fields, such as
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1027 `AS:i` and `XS:i`.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1028
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1029 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
1030 searches for at most `<int>` distinct, valid alignments for each read. The
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1031 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
1032 finds `<int>`, whichever happens first. All alignments found are reported in
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1033 descending order by alignment score. The alignment score for a paired-end
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1034 alignment equals the sum of the alignment scores of the individual mates. Each
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1035 reported read or pair alignment beyond the first has the SAM 'secondary' bit
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1036 (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
1037 `<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
1038 `<int>` alignments reported are the best possible in terms of alignment score.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1039 `-k` is mutually exclusive with `-a`.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1040
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1041 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1042 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1043
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1044 -a
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1045 Like `-k` but with no upper limit on number of alignments to search for. `-a`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1046 is mutually exclusive with `-k`.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1047
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1048 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1049 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
1050
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1051 -----
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1052
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1053 **Effort options**::
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1054
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1055 -D <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1056 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1057 moves on, using the alignments found so far. A seed extension "fails" if it
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1058 does not yield a new best or a new second-best alignment. This limit is
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1059 automatically adjusted up when -k or -a are specified. Default: 15.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1060
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1061 -R <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1062 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1063 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1064 (same length, same number of mismatches allowed) at different offsets and
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1065 searches for more alignments. A read is considered to have repetitive seeds if
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1066 the total number of seed hits divided by the number of seeds that aligned at
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1067 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
1068
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1069 -----
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1070
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1071 **Paired-end options**::
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1072
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1073 -I/--minins <int>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1074 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1075 specified and a paired-end alignment consists of two 20-bp alignments in the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1076 appropriate orientation with a 20-bp gap between them, that alignment is
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1077 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1078 be valid in that case. If trimming options `-3` or `-5` are also used, the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1079 `-I` constraint is applied with respect to the untrimmed mates.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1080
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1081 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1082 run. This is because larger differences bewteen `-I` and `-X` require that
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1083 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1084 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1085 efficient.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1086
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1087 Default: 0 (essentially imposing no minimum)
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1088
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1089 -X/--maxins <int>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1090 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1091 is specified and a paired-end alignment consists of two 20-bp alignments in the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1092 proper orientation with a 60-bp gap between them, that alignment is considered
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1093 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
1094 that case. If trimming options `-3` or `-5` are also used, the `-X`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1095 constraint is applied with respect to the untrimmed mates, not the trimmed
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1096 mates.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1097
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1098 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1099 run. This is because larger differences bewteen `-I` and `-X` require that
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1100 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1101 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1102 efficient.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1103
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1104 Default: 500.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1105
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1106 --fr/--rf/--ff
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1107 The upstream/downstream mate orientations for a valid paired-end alignment
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1108 against the forward reference strand. E.g., if `--fr` is specified and there is
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1109 a candidate paired-end alignment where mate 1 appears upstream of the reverse
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1110 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1111 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1112 complement of mate 1 and all other constraints are met, that too is valid.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1113 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1114 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1115 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1116 for Illumina's Paired-end Sequencing Assay).
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1117
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1118 --no-mixed
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1119 By default, when `bowtie2` cannot find a concordant or discordant alignment for
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1120 a pair, it then tries to find alignments for the individual mates. This option
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1121 disables that behavior.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1122
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1123 --no-discordant
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1124 By default, `bowtie2` looks for discordant alignments if it cannot find any
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1125 concordant alignments. A discordant alignment is an alignment where both mates
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1126 align uniquely, but that does not satisfy the paired-end constraints
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1127 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1128
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1129 --dovetail
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1130 If the mates "dovetail", that is if one mate alignment extends past the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1131 beginning of the other such that the wrong mate begins upstream, consider that
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
1132 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1133
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1134 --no-contain
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1135 If one mate alignment contains the other, consider that to be non-concordant.
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
1136 Default: a mate can contain the other in a concordant alignment.
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1137
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1138 --no-overlap
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1139 If one mate alignment overlaps the other at all, consider that to be
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
1140 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
1141
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1142 ------
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1143
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1144 **SAM options**::
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1145
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1146 --rg-id <text>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1147 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1148 printed, with `<text>` as the value associated with the `ID:` tag. It also
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1149 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
1150 value set to `<text>`.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1151
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1152 --rg <text>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1153 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1154 `@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
1155 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
1156 Specification. Specify `--rg` multiple times to set multiple fields. See the
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
1157 SAM Specification for details about what fields are legal.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1158
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1159 --omit-sec-seq
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1160 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1161 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1162 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
1163
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1164 -----
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1165
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1166 **Other options**::
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1167
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1168 --reorder
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1169 Guarantees that output SAM records are printed in an order corresponding to the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1170 order of the reads in the original input file, even when `-p` is set greater
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1171 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1172 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1173 not specified. Has no effect if `-p` is set to 1, since output order will
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1174 naturally correspond to input order in that case.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1175
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1176 --seed <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1177 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1178
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1179 --non-deterministic
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1180 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1181 seeds the generator with a number derived from (a) the read name, (b) the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1182 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1183 option. This means that if two reads are identical (same name, same
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1184 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1185 for both, even if there was ambiguity. When `--non-deterministic` is specified,
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1186 Bowtie 2 re-initializes its pseudo-random generator for each read using the
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1187 current time. This means that Bowtie 2 will not necessarily report the same
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1188 alignment for two identical reads. This is counter-intuitive for some users,
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1189 but might be more appropriate in situations where the input consists of many
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1190 identical reads.
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1191
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1192 -----
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1193
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1194
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1195 **Paired-end (and mate-pair) data in fastq format**
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1196
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1197 Paired end datasets can be represented as two individual datasets:
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1198
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1199 First dataset::
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1200
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1201 @1/1
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1202 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1203 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1204 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1205 @2/1
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1206 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1207 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1208 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1209
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1210 Second dataset::
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1211
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1212 @1/2
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1213 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1216 @2/2
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1217 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
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 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
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 @1/2
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1228 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1231 @2/1
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1232 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1235 @2/2
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1236 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1237 +
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
1238 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1239 ]]></help>
2
2a6cfe8997aa Uploaded from GH
devteam
parents: 1
diff changeset
1240 <citations>
17
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
1241 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
1242 <citation type="doi">10.1038/nmeth.1923</citation>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
iuc
parents: 16
diff changeset
1243 </citations>
0
a03a7ee6cdff Imported from capsule None
devteam
parents:
diff changeset
1244 </tool>