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Nanopolish variants tool metadata

Miscellaneous

Name: Nanopolish variants

Description: - Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences

Id: nanopolish_variants

Guid: toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/0.14.0+galaxy0

Version: 0.14.0+galaxy0

Version command string: None

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/0.14.0+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/0.13.2+galaxy0

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

nanopolish_variants

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

nanopolish

0.14.0

package

Functional tests

name

inputs

outputs

required files

Test-1

name: value
name: value

reads.fasta
fast5_files.tar.gz
reads.sorted.bam
draft_single_seq.fa
value

Test-2

input_merged: reads.fasta
input_reads_raw: fast5_files.tar.bz2
b: reads.sorted.bam
reference_source|ref_file: draft_single_seq.fa
reference_source|reference_source_selector: history
w: tig00000001:200000-202000

name: value
name: value

reads.fasta
fast5_files.tar.bz2
reads.sorted.bam
draft_single_seq.fa
value

Test-3

input_merged: reads.fasta
input_reads_raw: fast5_files.tar
b: reads.sorted.bam
reference_source|ref_file: draft_single_seq.fa
reference_source|reference_source_selector: history
w: tig00000001:200000-202000

name: value
name: value

reads.fasta
fast5_files.tar
reads.sorted.bam
draft_single_seq.fa
value

Test-4

input_merged: reads.fasta
input_reads_raw: fast5_files.tar.gz
b: reads.sorted.bam
reference_source|ref_file: draft_single_seq.fa
reference_source|reference_source_selector: history
w: tig00000001:198000-202000
ploidy: 2
min_flanking_sequence: 10
consensus: False
snps: True
faster: True
all_bases: True

name: value
name: value

reads.fasta
fast5_files.tar.gz
reads.sorted.bam
draft_single_seq.fa
value