Repository revision
19:dfd8b7f78c37

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

Map with BWA tool metadata
Miscellaneous
Map with BWA
- map short reads (< 100 bp) against reference genome
bwa
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.3
0.7.17.3
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.3 (this tool)
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.2
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.16.2
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.2
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.1
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.4.2
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.4.1
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.3.1
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.3.0
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.2.3
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.2.1
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.1
bwa
Requirements (dependencies defined in the <requirements> tag set)
name version type
bwa 0.7.17 package
samtools 1.6 package
Functional tests
name inputs outputs required files
Test-1 reference_source|reference_source_selector: history
input_type|input_type_selector: single
reference_source|ref_file: bwa-mem-mt-genome.fa
input_type|fastq_input1: bwa-mem-fasta1.fa
analysis_type|analysis_type_selector: illumina
bam_output: bwa-aln-test1-fasta.bam
bwa-mem-mt-genome.fa
bwa-mem-fasta1.fa
bwa-aln-test1-fasta.bam
Test-2 input_type|input_type_selector: paired
reference_source|reference_source_selector: history
input_type|fastq_input1: bwa-mem-fastq1.fq
input_type|fastq_input2: bwa-mem-fastq2.fq
analysis_type|analysis_type_selector: illumina
reference_source|ref_file: bwa-mem-mt-genome.fa
bam_output: bwa-aln-test1.bam
bwa-mem-mt-genome.fa
bwa-mem-fastq1.fq
bwa-mem-fastq2.fq
bwa-aln-test1.bam
Test-3 input_type|input_type_selector: paired
reference_source|reference_source_selector: history
input_type|fastq_input1: bwa-mem-fastq1.fq.gz
input_type|fastq_input2: bwa-mem-fastq2.fq
analysis_type|analysis_type_selector: illumina
reference_source|ref_file: bwa-mem-mt-genome.fa
bam_output: bwa-aln-test1.bam
bwa-mem-mt-genome.fa
bwa-mem-fastq1.fq.gz
bwa-mem-fastq2.fq
bwa-aln-test1.bam
Test-4 reference_source|reference_source_selector: history
input_type|input_type_selector: paired_bam
reference_source|ref_file: bwa-mem-mt-genome.fa
input_type|bam_input: bwa-aln-bam-input.bam
analysis_type|analysis_type_selector: illumina
bam_output: bwa-aln-test2.bam
bwa-mem-mt-genome.fa
bwa-aln-bam-input.bam
bwa-aln-test2.bam
Test-5 input_type|input_type_selector: paired
rg|rg_selector: set
rg|PL: CAPILLARY
analysis_type|analysis_type_selector: illumina
reference_source|reference_source_selector: history
reference_source|ref_file: bwa-mem-mt-genome.fa
rg|read_group_id_conditional|ID: rg1
input_type|fastq_input1: bwa-mem-fastq1.fq
input_type|fastq_input2: bwa-mem-fastq2.fq
bam_output: bwa-aln-test3.bam
bwa-mem-mt-genome.fa
bwa-mem-fastq1.fq
bwa-mem-fastq2.fq
bwa-aln-test3.bam