| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| 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 |
| Additional information about this tool |
#import re
#import os
#if str($mode.in.custom) == 'false'
#if $mode.mode == 'individual'
#set $labels = re.sub('[^\w\-_]', '_', str($mode.in.inputs.element_identifier))
#else
#set $labels = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $mode.in.inputs])
#end if
echo $labels &&
#else
#if $mode.mode == 'individual'
#if str($mode.in.labels) != ''
#set $labels = re.sub('[^\w\-_]', '_', str($mode.in.labels))
#else
#set $labels = re.sub('[^\w\-_]', '_', str($mode.in.input.element_identifier))
#end if
#else
#set $labels = []
#for $x in $mode.in.inputs
#if str($x.labels) != ''
#silent $labels.append(re.sub('[^\w\-_]', '_', str($x.labels)))
#else
#silent $labels.append(re.sub('[^\w\-_]', '_', str($x.input.element_identifier)))
#end if
#end for
#set $labels = ','.join($labels)
#end if
#end if
#if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list'
#set $temp_ref_list_fp = 'temp_ref_list'
#for $i in $assembly.ref.references_list.split(',')
echo $i >> $temp_ref_list_fp &&
#end for
#end if
#if $mode.reads.reads_option == 'paired'
#if $mode.mode == 'individual'
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
ln -s '$mode.reads.input_1' 'pe1-${identifier}.${mode.reads.input_1.ext}' &&
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_2.element_identifier))
ln -s '$mode.reads.input_2' 'pe2-${identifier}.${mode.reads.input_2.ext}' &&
#else
#for $read in $mode.reads.input_1
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
ln -s '$read' 'pe1-${identifier}.${read.ext}' &&
#end for
#for $read in $mode.reads.input_2
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
ln -s '$read' 'pe2-${identifier}.${read.ext}' &&
#end for
#end if
#else if $mode.reads.reads_option == 'paired_collection'
#if $mode.mode == 'individual'
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
ln -s '$mode.reads.input_1.forward' 'pe1-${identifier}.${mode.reads.input_1.forward.ext}' &&
ln -s '$mode.reads.input_1.reverse' 'pe2-${identifier}.${mode.reads.input_1.reverse.ext}' &&
#else
#for $read in $mode.reads.input_1
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
ln -s '$read.forward' 'pe1-${identifier}.${read.forward.ext}' &&
ln -s '$read.reverse' 'pe2-${identifier}.${read.reverse.ext}' &&
#end for
#end if
#end if
#if $assembly.type == 'genome'
quast
#else
metaquast
#end if
#if $mode.reads.reads_option == 'single'
#if $mode.mode == 'individual'
--single '$mode.reads.input_1'
#else
#for $read in $mode.reads.input_1
--single '$read'
#end for
#end if
#else if $mode.reads.reads_option == 'paired'
#if $mode.mode == 'individual'
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
--pe1 'pe1-${identifier}.${mode.reads.input_1.ext}'
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_2.element_identifier))
--pe2 'pe2-${identifier}.${mode.reads.input_2.ext}'
#else
#for $read in $mode.reads.input_1
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
--pe1 'pe1-${identifier}.${read.ext}'
#end for
#for $read in $mode.reads.input_2
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
--pe2 'pe2-${identifier}.${read.ext}'
#end for
#end if
#else if $mode.reads.reads_option == 'paired_collection'
#if $mode.mode == 'individual'
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
--pe1 'pe1-${identifier}.${mode.reads.input_1.forward.ext}'
--pe2 'pe2-${identifier}.${mode.reads.input_1.reverse.ext}'
#else
#for $read in $mode.reads.input_1
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
--pe1 'pe1-${identifier}.${read.forward.ext}'
--pe2 'pe2-${identifier}.${read.reverse.ext}'
#end for
#end if
#else if $mode.reads.reads_option == 'paired_interlaced'
#if $mode.mode == 'individual'
--pe12 '$mode.reads.input_1'
#else
#for $read in $mode.reads.input_1
--pe12 '$read'
#end for
#end if
#else if $mode.reads.reads_option == 'mate_paired'
#if $mode.mode == 'individual'
--mp1 '$mode.reads.input_1'
--mp2 '$mode.reads.input_2'
#else
#for $read in $mode.reads.input_1
--mp1 '$read'
#end for
#for $read in $mode.reads.input_2
--mp2 '$read'
#end for
#end if
#else if $mode.reads.reads_option == 'pacbio'
#if $mode.mode == 'individual'
--pacbio '$mode.reads.input_1'
#else
#for $read in $mode.reads.input_1
--pacbio '$read'
#end for
#end if
#else if $mode.reads.reads_option == 'nanopore'
#if $mode.mode == 'individual'
--nanopore '$mode.reads.input_1'
#else
#for $read in $mode.reads.input_1
--nanopore '$read'
#end for
#end if
#end if
--labels '$labels'
-o 'outputdir'
#if $assembly.type == 'genome'
#if $assembly.ref.use_ref == 'true'
-r '$assembly.ref.r'
#if $assembly.ref.features
--features '$assembly.ref.features'
#end if
#if $assembly.ref.operons
--operons '$assembly.ref.operons'
#end if
$assembly.ref.circos
$assembly.ref.k_mer.k_mer_stats
#if str($assembly.ref.k_mer.k_mer_stats) != ''
--k-mer-size $assembly.ref.k_mer.k_mer_size
#end if
#else if $assembly.ref.est_ref_size
--est-ref-size $assembly.ref.est_ref_size
#end if
$assembly.orga_type
#else if $assembly.type == 'metagenome'
#if $assembly.ref.origin == 'history'
-r '$assembly.ref.r'
#else if $assembly.ref.origin == 'list'
--references-list '$temp_ref_list_fp'
#else if $assembly.ref.origin == 'silva'
--max-ref-num $assembly.ref.max_ref_num
#end if
$assembly.reuse_combined_alignments
#end if
--min-identity $assembly.min_identity
--min-contig $min_contig
$split_scaffolds
$large
#if str($genes.gene_finding.tool) != 'none'
$genes.gene_finding.tool
#if $genes.gene_finding.tool == '--gene_finding' or $genes.gene_finding.tool == '--glimmer'
#set $gene_threshold = ','.join([x.strip() for x in str($genes.gene_finding.gene_thresholds).split(',')])
--gene-thresholds '$gene_threshold'
#end if
#end if
$genes.rna_finding
$genes.conserved_genes_finding
$alignments.use_all_alignments
--min-alignment $alignments.min_alignment
--ambiguity-usage '$alignments.ambiguity_usage'
--ambiguity-score $alignments.ambiguity_score
$alignments.fragmented
$alignments.upper_bound_assembly
#if $alignments.upper_bound_min_con
--upper-bound-min-con $alignments.upper_bound_min_con
#end if
#if $alignments.local_mis_size
--local-mis-size $alignments.local_mis_size
#end if
#if $alignments.fragmented
#if $advanced.fragmented_max_indent != ''
--fragmented-max-indent $advanced.fragmented_max_indent
#end if
#end if
#set $contig_thresholds = ','.join([x.strip() for x in str($advanced.contig_thresholds).split(',')])
--contig-thresholds '$contig_thresholds'
$advanced.strict_NA
--extensive-mis-size $advanced.extensive_mis_size
--scaffold-gap-max-size $advanced.scaffold_gap_max_size
--unaligned-part-size $advanced.unaligned_part_size
$advanced.skip_unaligned_mis_contigs
$advanced.report_all_metrics
--x-for-Nx $advanced.x_for_Nx
#if str($mode.in.custom) == 'false'
#if $mode.mode == 'individual'
'$mode.in.inputs'
#else
#for $k in $mode.in.inputs
'$k'
#end for
#end if
#else
#if $mode.mode == 'individual'
'$mode.in.input'
#else
#for $k in $mode.in.inputs
'$k.input'
#end for
#end if
#end if
--threads \${GALAXY_SLOTS:-1}
#if $assembly.type == 'genome'
&& mkdir -p '$report_html.files_path'
&& cp outputdir/*.html '$report_html.files_path'
#if $assembly.ref.use_ref
&& cp -R outputdir/icarus_viewers '$report_html.files_path'
#end if
#else
&& if [[ -f "outputdir/report.tsv" ]]; then mkdir -p "outputdir/combined_reference/" && cp "outputdir/report.tsv" "outputdir/combined_reference/report.tsv"; fi
&& if [[ -f "outputdir/report.html" ]]; then mkdir -p "outputdir/combined_reference/" && cp outputdir/*.html "outputdir/combined_reference/"; fi
&& mkdir -p '$report_html_meta.files_path'
&& cp outputdir/combined_reference/*.html '$report_html_meta.files_path'
&& if [[ -d "outputdir/icarus_viewers" ]]; then cp -R outputdir/icarus_viewers 'outputdir/combined_reference/'; fi
&& if [[ -d "outputdir/combined_reference/icarus_viewers" ]]; then cp -R outputdir/combined_reference/icarus_viewers '$report_html_meta.files_path'; fi
&& if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p '$krona.files_path' && cp outputdir/krona_charts/*.html '$krona.files_path'; fi
#end if
| 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 |