Repository revision
3:bc79b5b0fe04

Repository 'nanopolish_variants'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants

Nanopolish variants tool metadata
Miscellaneous
- Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences
nanopolish_variants
toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/0.1.0
0.1.0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/0.11.1
toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/0.1.0 (this tool)
nanopolish_variants
Requirements (dependencies defined in the <requirements> tag set)
name version type
nanopolish 0.11.1 package
Functional tests
name inputs outputs required files
Test-1 input_merged: reads.fasta
input_reads_raw: fast5_files.tar.gz
reference_source|reference_source_selector: history
b: reads.sorted.bam
w: tig00000001:200000-202000
reference_source|ref_file: draft_single_seq.fa
attributes: name
attributes: name
reads.fasta
fast5_files.tar.gz
reads.sorted.bam
draft_single_seq.fa
name
Test-2 input_merged: reads.fasta
input_reads_raw: fast5_files.tar.bz2
reference_source|reference_source_selector: history
b: reads.sorted.bam
w: tig00000001:200000-202000
reference_source|ref_file: draft_single_seq.fa
attributes: name
attributes: name
reads.fasta
fast5_files.tar.bz2
reads.sorted.bam
draft_single_seq.fa
name
Test-3 input_merged: reads.fasta
input_reads_raw: fast5_files.tar
reference_source|reference_source_selector: history
b: reads.sorted.bam
w: tig00000001:200000-202000
reference_source|ref_file: draft_single_seq.fa
attributes: name
attributes: name
reads.fasta
fast5_files.tar
reads.sorted.bam
draft_single_seq.fa
name
Test-4 min_flanking_sequence: 10
input_merged: reads.fasta
faster: True
input_reads_raw: fast5_files.tar.gz
reference_source|reference_source_selector: history
consensus: False
snps: True
b: reads.sorted.bam
w: tig00000001:198000-202000
reference_source|ref_file: draft_single_seq.fa
ploidy: 2
all_bases: True
attributes: name
attributes: name
reads.fasta
fast5_files.tar.gz
reads.sorted.bam
draft_single_seq.fa
name