Galaxy |

ARTIC minion tool metadata

Miscellaneous

Name: ARTIC minion

Description: Build consensus sequence and call variants from amplicon-based nanopore sequence data

Id: artic_minion

Guid: toolshed.g2.bx.psu.edu/repos/iuc/artic_minion/artic_minion/1.2.1+galaxy0

Version: 1.2.1+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/iuc/artic_minion/artic_minion/1.2.3+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/artic_minion/artic_minion/1.2.1+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/artic_minion/artic_minion/1.1.3+galaxy2

toolshed.g2.bx.psu.edu/repos/iuc/artic_minion/artic_minion/1.1.3+galaxy1

toolshed.g2.bx.psu.edu/repos/iuc/artic_minion/artic_minion/1.1.3+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/artic_minion/artic_minion/1.1.2+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/artic_minion/artic_minion/1.1.0_rc2+galaxy0

artic_minion

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

Requirements:

name

version

type

artic

1.2.1

package

Additional information about this tool

Command:

mkdir -p 'scheme/name/V1' &&
        #if str( $primer_scheme_source.primer_scheme_source_selector ) == "tool_data_table":
          ln -s '${primer_scheme_source.primer_scheme_bedfile.fields.path}' 'scheme/name/V1/name.scheme.bed' &&
        #else:
          ln -s '${primer_scheme_source.primer_scheme_bedfile}' 'scheme/name/V1/name.scheme.bed' &&
        #end if
        #if str( $reference_source.reference_source_selector ) == "history":
          ln -s '${reference_source.reference}' 'scheme/name/V1/name.reference.fasta' &&
          samtools faidx 'scheme/name/V1/name.reference.fasta' &&
        #else:
          ln -s '${reference_source.reference.fields.path}' 'scheme/name/V1/name.reference.fasta' &&
          samtools faidx 'scheme/name/V1/name.reference.fasta' &&
        #end if
        artic minion
            --threads \${GALAXY_SLOTS:-1}
        #if $normalise > 0:
            --normalise ${normalise}
        #end if
            --read-file '${read_file}'
            --scheme-directory 'scheme'
            --medaka
            --medaka-model '$medaka_model'
            $bwa
            'name/V1'
            ## enclose the sample name in extra single quotes because
            ## the minion pipeline script doesn't care about passing
            ## its arguments safely.
            "'"'${read_file.element_identifier}'"'"
        && bgzip -f '${read_file.element_identifier}.fail.vcf'
        ## remove enclosing single-quotes from header of output consensus fasta
        && sed -i "1s/'${read_file.element_identifier}'/${read_file.element_identifier}/" '${read_file.element_identifier}.consensus.fasta'

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

read_file: SRR11410539_seqtk_sample_500_1.fastq
primer_scheme_source|primer_scheme_bedfile: test_entry
primer_scheme_source|primer_scheme_source_selector: tool_data_table
reference_source|reference: nCoV-2019.reference.fasta
reference_source|reference_source_selector: history
medaka_model: r941_min_high_g360

name: value

SRR11410539_seqtk_sample_500_1.fastq
nCoV-2019.reference.fasta
value

Test-2

read_file: SRR11410539_seqtk_sample_500_1.fastq
primer_scheme_source|primer_scheme_bedfile: nCoV-2019.scheme.V1.bed
primer_scheme_source|primer_scheme_source_selector: history
reference_source|reference: nCoV-2019.reference.fasta
reference_source|reference_source_selector: history
medaka_model: r941_min_high_g360

name: value

SRR11410539_seqtk_sample_500_1.fastq
nCoV-2019.scheme.V1.bed
nCoV-2019.reference.fasta
value

Test-3

name: value

SRR11410539_seqtk_sample_500_1.fastq
value