| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy5 |
| 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 |
| 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 | 5.2.0 | package |
| bwa | 0.7.17 | package |
| bedtools | 2.30.0 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
mode|in|inputs_0|input: contigs1.fna mode|in|inputs_0|labels: contig1 mode|in|inputs_1|input: contigs2.fna mode|in|inputs_1|labels: contig2 mode|in|custom: true mode|mode: co 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|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 |
mode|in|inputs_0|input: contigs1.fna mode|in|inputs_0|labels: contig1 mode|in|inputs_1|input: contigs2.fna mode|in|inputs_1|labels: contig2 mode|in|custom: true mode|mode: co 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 |
mode|in|inputs: contigs1.fna mode|in|custom: false mode|mode: individual assembly|ref|use_ref: false assembly|orga_type: --eukaryote assembly|min_identity: 95.0 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|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 value |
| Test-4 |
mode|in|inputs: contigs3.fasta mode|in|custom: false mode|mode: individual assembly|ref|max_ref_num: 50 assembly|ref|origin: silva 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|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: ['log', 'html', 'tabular'] |
name: value name: value name: value |
contigs3.fasta value |
| Test-5 |
mode|in|inputs_0|input: contigs1.fna mode|in|inputs_0|labels: contig1 mode|in|inputs_1|input: contigs2.fna mode|in|inputs_1|labels: contig2 mode|in|custom: true mode|reads|input_1: ['pacbio_01.fastq', 'pacbio_02.fastq', 'pacbio_03.fastq', 'pacbio_04.fastq'] mode|reads|reads_option: pacbio mode|mode: co 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 |
mode|in|inputs_0|input: contigs1.fna mode|in|inputs_0|labels: contig1 mode|in|inputs_1|input: contigs2.fna mode|in|inputs_1|labels: contig2 mode|in|custom: true mode|reads|input_1: ['pacbio_01.fastq.gz', 'pacbio_02.fastq.gz'] mode|reads|reads_option: single mode|mode: co output_files: tabular |
name: value |
contigs1.fna contigs2.fna pacbio_01.fastq.gz pacbio_02.fastq.gz value |
| Test-7 |
mode|in|inputs_0|input: contigs1.fna mode|in|inputs_0|labels: contig1 mode|in|inputs_1|input: contigs2.fna mode|in|inputs_1|labels: contig2 mode|in|custom: true mode|reads|input_1: ['pacbio_01.fasta.gz', 'pacbio_02.fasta.gz'] mode|reads|reads_option: single mode|mode: co output_files: tabular |
name: value |
contigs1.fna contigs2.fna pacbio_01.fasta.gz pacbio_02.fasta.gz value |
| Test-8 |
mode|in|inputs_0|input: meta_contigs_1.fasta mode|in|inputs_0|labels: meta_contigs_1 mode|in|inputs_1|input: meta_contigs_2.fasta mode|in|inputs_1|labels: meta_contigs_2 mode|mode: co assembly|ref|r: ['meta_ref_1.fasta', 'meta_ref_2.fasta', 'meta_ref_3.fasta'] assembly|ref|origin: history assembly|min_identity: 95.0 assembly|type: metagenome 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|ambiguity_usage: one alignments|ambiguity_score: 0.99 alignments|fragmented: False advanced|contig_thresholds: 0,1000 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', 'summary'] |
name: value |
meta_contigs_1.fasta meta_contigs_2.fasta meta_ref_1.fasta meta_ref_2.fasta meta_ref_3.fasta value |
| Test-9 |
mode|in|inputs_0|input: meta_contigs_1.fasta mode|in|inputs_0|labels: meta_contigs_1 mode|in|inputs_1|input: meta_contigs_2.fasta mode|in|inputs_1|labels: meta_contigs_2 mode|mode: co assembly|ref|references_list: Lactobacillus_delbrueckii_bulgaricus,Lactobacillus_reuteri assembly|ref|origin: list assembly|min_identity: 95.0 assembly|type: metagenome 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|ambiguity_usage: all alignments|ambiguity_score: 0.99 alignments|fragmented: False advanced|contig_thresholds: 0,1000 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', 'log'] |
name: value name: value |
meta_contigs_1.fasta meta_contigs_2.fasta value |
| Test-10 |
mode|in|inputs_0|input: contigs1.fna mode|in|inputs_0|labels: contig1 mode|in|inputs_1|input: contigs2.fna mode|in|inputs_1|labels: contig2 mode|in|custom: true mode|mode: co assembly|ref|use_ref: false assembly|type: genome alignments|local_mis_size: 210 advanced|report_all_metrics: True advanced|x_for_Nx: 80 output_files: tabular |
name: value |
contigs1.fna contigs2.fna value |
| Test-11 |
mode|in|input: contigs1.fna mode|in|labels: contig1 mode|in|custom: true mode|reads|input_1: reads1.fastq.gz mode|reads|input_2: reads2.fastq.gz mode|reads|reads_option: paired mode|mode: individual assembly|ref|use_ref: false assembly|type: genome output_files: tabular |
name: value |
contigs1.fna reads1.fastq.gz reads2.fastq.gz value |
| Test-12 |
mode|in|input: contigs1.fna mode|in|labels: contig1 mode|in|custom: true mode|reads|input_1: paired collection mode|reads|reads_option: paired_collection mode|mode: individual assembly|ref|use_ref: false assembly|type: genome output_files: tabular |
name: value |
contigs1.fna reads1.fastq.gz reads2.fastq.gz value |
| Test-13 |
mode|in|inputs: ['contigs1.fna', 'contigs2.fna'] mode|in|custom: false mode|reads|input_1: list:paired collection mode|reads|reads_option: paired_collection mode|mode: co assembly|ref|use_ref: false assembly|type: genome output_files: tabular |
name: value |
contigs1.fna contigs2.fna reads1.fastq.gz reads2.fastq.gz value |