Galaxy |

bcftools consensus tool metadata

Miscellaneous

Name: bcftools consensus

Description: Create consensus sequence by applying VCF variants to a reference fasta file

Id: bcftools_consensus

Guid: toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2

Version: 1.9+galaxy2

Version command string: bcftools 2>&1 | grep 'Version:'

Display in tool panel: True

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

toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10

toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy2 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9+galaxy1

toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.9

toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.4.0

toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.3.1

toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.3.0

bcftools_consensus

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

Requirements:

name

version

type

bcftools

1.9

package

htslib

1.9

package

samtools

1.9

package

gawk

5.0.1

package

Functional tests

name

inputs

outputs

required files

Test-1

input_file: consensus.vcf
reference_source|fasta_ref: consensus.fa
reference_source|reference_source_selector: history
sec_default|mask: consensus.tab
chain: True

name: value
name: value

consensus.vcf
consensus.fa
consensus.tab
value

Test-2

input_file: consensus.vcf
reference_source|fasta_ref: consensus
reference_source|reference_source_selector: cached
sec_default|mask: consensus.tab
chain: True

name: value
name: value

consensus.vcf
consensus.tab
value

Test-3

input_file: consensus.vcf
reference_source|fasta_ref: consensus.fa
reference_source|reference_source_selector: history
sec_default|mask: consensus.tab
chain: False
rename: True

name: value

consensus.vcf
consensus.fa
consensus.tab
value