| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.1 |
| bwa_mem |
| 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 fastq_input|fastq_input1: bwa-mem-fastq1.fq fastq_input|fastq_input2: bwa-mem-fastq2.fq analysis_type|analysis_type_selector: illumina reference_source|ref_file: bwa-mem-mt-genome.fa fastq_input|fastq_input_selector: paired |
bam_output: bwa-mem-test1.bam |
bwa-mem-mt-genome.fa bwa-mem-fastq1.fq bwa-mem-fastq2.fq bwa-mem-test1.bam |
| Test-2 |
reference_source|reference_source_selector: history fastq_input|fastq_input1: bwa-mem-fasta1.fa reference_source|ref_file: bwa-mem-mt-genome.fa fastq_input|fastq_input_selector: single analysis_type|analysis_type_selector: illumina |
bam_output: bwa-mem-test1-fasta.bam |
bwa-mem-mt-genome.fa bwa-mem-fasta1.fa bwa-mem-test1-fasta.bam |
| Test-3 |
reference_source|reference_source_selector: history fastq_input|fastq_input1: bwa-mem-fastq1.fq.gz fastq_input|fastq_input2: bwa-mem-fastq2.fq analysis_type|analysis_type_selector: illumina reference_source|ref_file: bwa-mem-mt-genome.fa fastq_input|fastq_input_selector: paired |
bam_output: bwa-mem-test1.bam |
bwa-mem-mt-genome.fa bwa-mem-fastq1.fq.gz bwa-mem-fastq2.fq bwa-mem-test1.bam |
| Test-4 |
reference_source|reference_source_selector: history fastq_input|fastq_input1: bwa-mem-fastq1.fq fastq_input|fastq_input2: bwa-mem-fastq2.fq rg|read_group_id_conditional|ID: rg1 analysis_type|analysis_type_selector: illumina reference_source|index_a: is rg|read_group_lb_conditional|LB: AARDVARK-1 rg|rg_selector: set reference_source|ref_file: bwa-mem-mt-genome.fa fastq_input|fastq_input_selector: paired rg|PL: CAPILLARY |
bam_output: bwa-mem-test2.bam |
bwa-mem-mt-genome.fa bwa-mem-fastq1.fq bwa-mem-fastq2.fq bwa-mem-test2.bam |