Repository revision
17:66f992977578

Repository 'bowtie2'
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/bowtie2

Bowtie2 tool metadata
Miscellaneous
Bowtie2
- map reads against reference genome
bowtie2
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.2.2
2.3.2.2
bowtie2 --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.3.1
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.2.2 (this tool)
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.2.1
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0.1
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.0
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.8
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.6
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.5
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.4
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.3
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.2
bowtie2
Requirements (dependencies defined in the <requirements> tag set)
name version type
bowtie2 2.3.2 package
samtools 1.3.1 package
Functional tests
name inputs outputs required files
Test-1 library|input_1: bowtie2-fq1.fq
library|input_2: bowtie2-fq2.fq
library|unaligned_file: False
library|paired_options|paired_options_selector: no
library|type: paired
reference_genome|own_file: bowtie2-ref.fasta
reference_genome|source: history
analysis_type|analysis_type_selector: simple
name: value
bowtie2-fq1.fq
bowtie2-fq2.fq
bowtie2-ref.fasta
value
Test-2 library|input_1: paired collection
library|unaligned_file: False
library|paired_options|paired_options_selector: no
library|type: paired_collection
reference_genome|own_file: bowtie2-ref.fasta
reference_genome|source: history
analysis_type|analysis_type_selector: simple
name: value
bowtie2-fq1.fq
bowtie2-fq2.fq
bowtie2-ref.fasta
value
Test-3 library|input_1: bowtie2-fq1.fq
library|input_2: bowtie2-fq2.fq
library|unaligned_file: False
library|paired_options|paired_options_selector: no
library|type: paired
reference_genome|own_file: bowtie2-ref.fasta
reference_genome|source: history
rg|read_group_id_conditional|ID: rg1
rg|PL: CAPILLARY
rg|rg_selector: set
analysis_type|analysis_type_selector: simple
name: value
bowtie2-fq1.fq
bowtie2-fq2.fq
bowtie2-ref.fasta
value
Test-4 library|input_1: bowtie2-fq1.fq
library|input_2: bowtie2-fq2.fq
library|unaligned_file: False
library|paired_options|paired_options_selector: no
library|type: paired
reference_genome|own_file: bowtie2-ref.fasta
reference_genome|source: history
analysis_type|analysis_type_selector: simple
save_mapping_stats: True
name: value
name: value
bowtie2-fq1.fq
bowtie2-fq2.fq
bowtie2-ref.fasta
value
Test-5 library|input_1: bowtie2-fq_il.fq
library|unaligned_file: False
library|type: paired_interleaved
reference_genome|own_file: bowtie2-ref.fasta
reference_genome|source: history
rg|read_group_id_conditional|ID: rg1
rg|PL: CAPILLARY
rg|rg_selector: set
analysis_type|analysis_type_selector: simple
name: value
bowtie2-fq_il.fq
bowtie2-ref.fasta
value
Test-6 library|input_1: bowtie2-fq1.fq.gz
library|input_2: bowtie2-fq2.fq.gz
library|unaligned_file: False
library|paired_options|paired_options_selector: no
library|type: paired
reference_genome|own_file: bowtie2-ref.fasta
reference_genome|source: history
analysis_type|analysis_type_selector: simple
name: value
bowtie2-fq1.fq.gz
bowtie2-fq2.fq.gz
bowtie2-ref.fasta
value
Test-7 library|input_1: bowtie2-fq1.fq.bz2
library|input_2: bowtie2-fq2.fq.bz2
library|unaligned_file: False
library|paired_options|paired_options_selector: no
library|type: paired
reference_genome|own_file: bowtie2-ref.fasta
reference_genome|source: history
analysis_type|analysis_type_selector: simple
name: value
bowtie2-fq1.fq.bz2
bowtie2-fq2.fq.bz2
bowtie2-ref.fasta
value
Test-8 library|input_1: bowtie2-fq1.fa
library|input_2: bowtie2-fq2.fa
library|unaligned_file: False
library|paired_options|paired_options_selector: no
library|type: paired
reference_genome|own_file: bowtie2-ref.fasta
reference_genome|source: history
analysis_type|analysis_type_selector: simple
name: value
bowtie2-fq1.fa
bowtie2-fq2.fa
bowtie2-ref.fasta
value