Repository revision
11:7594365c546b

Repository 'quast'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/quast

Quast tool metadata
Miscellaneous
Quast
Genome assembly Quality
quast
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3
5.0.2+galaxy3
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy4
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.6.3
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.5
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.1.1
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.1
quast
Requirements (dependencies defined in the <requirements> tag set)
name version type
quast 5.0.2 package
circos 0.69.8 package
Functional tests
name inputs outputs required files
Test-1 in|inputs_0|input: contigs1.fna
in|inputs_0|labels: contig1
in|inputs_1|input: contigs2.fna
in|inputs_1|labels: contig2
in|custom: true
assembly|ref|r: reference.fna
assembly|ref|features: genes.gff
assembly|ref|operons: operons.bed
assembly|ref|k_mer|k_mer_size: 101
assembly|ref|k_mer|k_mer_stats: --k-mer-stats
assembly|ref|circos: True
assembly|ref|use_ref: true
assembly|orga_type:
assembly|type: genome
min_contig: 500
split_scaffolds: False
genes|rna_finding: True
genes|conserved_genes_finding: True
alignments|use_all_alignments: True
alignments|min_alignment: 65
alignments|min_identity: 95.0
alignments|ambiguity_usage: one
alignments|ambiguity_score: 0.99
advanced|contig_thresholds: 0,1000
advanced|strict_NA: True
advanced|extensive_mis_size: 1000
advanced|scaffold_gap_max_size: 1000
advanced|unaligned_part_size: 500
advanced|skip_unaligned_mis_contigs: True
advanced|fragmented_max_indent: 50
output_files: html
name: value
name: value
contigs1.fna
contigs2.fna
reference.fna
genes.gff
operons.bed
value
Test-2 in|inputs_0|input: contigs1.fna
in|inputs_0|labels: contig1
in|inputs_1|input: contigs2.fna
in|inputs_1|labels: contig2
in|custom: true
assembly|ref|r: reference.fna
assembly|ref|features: genes.gff
assembly|ref|operons: operons.bed
assembly|ref|k_mer|k_mer_size: 101
assembly|ref|k_mer|k_mer_stats: --k-mer-stats
assembly|ref|circos: True
assembly|ref|use_ref: true
assembly|type: genome
output_files: ['html', 'pdf', 'tabular', 'log']
name: value
name: value
name: value
name: value
name: value
name: value
name: value
name: value
contigs1.fna
contigs2.fna
reference.fna
genes.gff
operons.bed
value
Test-3 in|inputs: ['contigs1.fna', 'contigs2.fna']
in|custom: false
assembly|ref|use_ref: false
assembly|orga_type: --eukaryote
assembly|type: genome
min_contig: 500
split_scaffolds: False
large: False
genes|gene_finding|tool: none
genes|rna_finding: False
genes|conserved_genes_finding: False
alignments|use_all_alignments: False
alignments|min_alignment: 65
alignments|min_identity: 95.0
alignments|ambiguity_usage: one
alignments|ambiguity_score: 0.99
alignments|fragmented: False
advanced|contig_thresholds: 0,1000, 500
advanced|strict_NA: False
advanced|extensive_mis_size: 1000
advanced|scaffold_gap_max_size: 1000
advanced|unaligned_part_size: 500
advanced|skip_unaligned_mis_contigs: False
output_files: ['html', 'pdf', 'log']
name: value
name: value
name: value
contigs1.fna
contigs2.fna
value
Test-4 in|inputs: contigs3.fasta
in|custom: false
assembly|ref|origin: none
assembly|type: metagenome
min_contig: 500
split_scaffolds: False
large: False
genes|gene_finding|tool: --mgm
genes|rna_finding: False
genes|conserved_genes_finding: False
alignments|use_all_alignments: False
alignments|min_alignment: 65
alignments|min_identity: 95.0
alignments|ambiguity_usage: one
alignments|ambiguity_score: 0.99
alignments|fragmented: False
advanced|contig_thresholds: 0,1000, 500
advanced|strict_NA: False
advanced|extensive_mis_size: 1000
advanced|scaffold_gap_max_size: 1000
advanced|unaligned_part_size: 500
advanced|skip_unaligned_mis_contigs: False
output_files: tabular
name: value
contigs3.fasta
value
Test-5 in|inputs_0|input: contigs1.fna
in|inputs_0|labels: contig1
in|inputs_1|input: contigs2.fna
in|inputs_1|labels: contig2
in|custom: true
reads|input_1: ['pacbio_01.fastq', 'pacbio_02.fastq', 'pacbio_03.fastq', 'pacbio_04.fastq']
reads|reads_option: pacbio
assembly|ref|r: reference.fna
assembly|ref|use_ref: true
assembly|type: genome
alignments|upper_bound_assembly: True
alignments|upper_bound_min_con: 1
output_files: tabular
name: value
name: value
name: value
contigs1.fna
contigs2.fna
pacbio_01.fastq
pacbio_02.fastq
pacbio_03.fastq
pacbio_04.fastq
reference.fna
value
Test-6 in|inputs_0|input: contigs1.fna
in|inputs_0|labels: contig1
in|inputs_1|input: contigs2.fna
in|inputs_1|labels: contig2
in|custom: true
reads|input_1: ['pacbio_01.fastq.gz', 'pacbio_02.fastq.gz']
reads|reads_option: single
output_files: tabular
name: value
contigs1.fna
contigs2.fna
pacbio_01.fastq.gz
pacbio_02.fastq.gz
value