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comparison quast.xml @ 14:3061c8b029e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
author iuc
date Fri, 05 Aug 2022 15:21:27 +0000
parents 675488238c96
children 72472698a2df
comparison
equal deleted inserted replaced
13:675488238c96 14:3061c8b029e5
1 <tool id="quast" name="Quast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> 1 <tool id="quast" name="Quast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Genome assembly Quality</description> 2 <description>Genome assembly Quality</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
10 #import re 10 #import re
11 #import os 11 #import os
12 12
13 #if str($in.custom) == 'false' 13 #if str($in.custom) == 'false'
14 #set $labels = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $in.inputs]) 14 #set $labels = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $in.inputs])
15 echo $labels && 15 echo $labels &&
16 #else 16 #else
17 #set $labels = [] 17 #set $labels = []
18 #for $x in $in.inputs 18 #for $x in $in.inputs
19 #if str($x.labels) != '' 19 #if str($x.labels) != ''
20 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.labels))) 20 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.labels)))
24 #end for 24 #end for
25 #set $labels = ','.join($labels) 25 #set $labels = ','.join($labels)
26 #end if 26 #end if
27 27
28 #if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list' 28 #if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list'
29 #set $temp_ref_list_fp = 'temp_ref_list_fp' 29 #set $temp_ref_list_fp = 'temp_ref_list'
30 #set $temp_ref_list_f = open($temp_ref_list_fp, 'w') 30 #for $i in $assembly.ref.references_list.split(',')
31 #silent $temp_ref_list_f.write('\n'.join([x.strip() for x in $assembly.ref.references_list.split(',')])) 31 echo $i >> $temp_ref_list_fp &&
32 #silent $temp_ref_list_f.close() 32 #end for
33 #end if
34
35 #if $reads.reads_option == 'paired'
36 #for $read in $reads.input_1
37 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
38 ln -s '$read' 'pe1-${identifier}.${read.ext}' &&
39 #end for
40 #for $read in $reads.input_2
41 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
42 ln -s '$read' 'pe2-${identifier}.${read.ext}' &&
43 #end for
44 #else if $reads.reads_option == 'paired_collection'
45 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($reads.input_1.element_identifier))
46 ln -s '$reads.input_1.forward' 'pe1-${identifier}.${reads.input_1.forward.ext}' &&
47 ln -s '$reads.input_1.reverse' 'pe2-${identifier}.${reads.input_1.reverse.ext}' &&
33 #end if 48 #end if
34 49
35 #if $assembly.type == 'genome' 50 #if $assembly.type == 'genome'
36 quast 51 quast
37 #else 52 #else
38 metaquast 53 metaquast
39 #end if 54 #end if
40 55
41 #if $reads.reads_option == 'single' 56 #if $reads.reads_option == 'single'
42 #for $read in $reads.input_1 57 #for $read in $reads.input_1
43 --single '$read' 58 --single '$read'
44 #end for 59 #end for
45 #else if $reads.reads_option == 'paired' 60 #else if $reads.reads_option == 'paired'
46 #for $read in $reads.input_1 61 #for $read in $reads.input_1
47 --pe1 '$read' 62 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
63 --pe1 'pe1-${identifier}.${read.ext}'
48 #end for 64 #end for
49 #for $read in $reads.input_2 65 #for $read in $reads.input_2
50 --pe2 '$read' 66 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
51 #end for 67 --pe2 'pe2-${identifier}.${read.ext}'
68 #end for
69 #else if $reads.reads_option == 'paired_collection'
70 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($reads.input_1.element_identifier))
71 --pe1 'pe1-${identifier}.${reads.input_1.forward.ext}'
72 --pe2 'pe2-${identifier}.${reads.input_1.reverse.ext}'
52 #else if $reads.reads_option == 'paired_interlaced' 73 #else if $reads.reads_option == 'paired_interlaced'
53 #for $read in $reads.input_1 74 #for $read in $reads.input_1
54 --pe12 '$read' 75 --pe12 '$read'
55 #end for 76 #end for
56 #else if $reads.reads_option == 'mate_paired' 77 #else if $reads.reads_option == 'mate_paired'
57 #for $read in $reads.input_1 78 #for $read in $reads.input_1
58 --mp1 '$read' 79 --mp1 '$read'
59 #end for 80 #end for
60 #for $read in $reads.input_2 81 #for $read in $reads.input_2
61 --mp2 '$read' 82 --mp2 '$read'
62 #end for 83 #end for
63 #else if $reads.reads_option == 'pacbio' 84 #else if $reads.reads_option == 'pacbio'
64 #for $read in $reads.input_1 85 #for $read in $reads.input_1
65 --pacbio '$read' 86 --pacbio '$read'
66 #end for 87 #end for
67 #else if $reads.reads_option == 'nanopore' 88 #else if $reads.reads_option == 'nanopore'
68 #for $read in $reads.input_1 89 #for $read in $reads.input_1
69 --nanopore '$read' 90 --nanopore '$read'
70 #end for 91 #end for
71 #end if 92 #end if
72 93
73 --labels '$labels' 94 --labels '$labels'
74 -o 'outputdir' 95 -o 'outputdir'
75 96
76 #if $assembly.type == 'genome' 97 #if $assembly.type == 'genome'
77 #if $assembly.ref.use_ref == 'true' 98 #if $assembly.ref.use_ref == 'true'
78 -r '$assembly.ref.r' 99 -r '$assembly.ref.r'
79 #if $assembly.ref.features 100 #if $assembly.ref.features
80 --features '$assembly.ref.features' 101 --features '$assembly.ref.features'
81 #end if 102 #end if
82 #if $assembly.ref.operons 103 #if $assembly.ref.operons
83 --operons '$assembly.ref.operons' 104 --operons '$assembly.ref.operons'
84 #end if 105 #end if
85 $assembly.ref.circos 106 $assembly.ref.circos
86 $assembly.ref.k_mer.k_mer_stats 107 $assembly.ref.k_mer.k_mer_stats
87 #if str($assembly.ref.k_mer.k_mer_stats) != '' 108 #if str($assembly.ref.k_mer.k_mer_stats) != ''
88 --k-mer-size $assembly.ref.k_mer.k_mer_size 109 --k-mer-size $assembly.ref.k_mer.k_mer_size
89 #end if 110 #end if
90 #else if $assembly.ref.est_ref_size 111 #else if $assembly.ref.est_ref_size
91 --est-ref-size $assembly.ref.est_ref_size 112 --est-ref-size $assembly.ref.est_ref_size
92 #end if 113 #end if
93 $assembly.orga_type 114 $assembly.orga_type
94 #else 115 #else if $assembly.type == 'metagenome'
95 #if $assembly.ref.origin == 'history' 116 #if $assembly.ref.origin == 'history'
96 -r '$assembly.ref.r' 117 -r '$assembly.ref.r'
97 #else if $assembly.ref.origin == 'list' 118 #else if $assembly.ref.origin == 'list'
98 --references-list '$temp_ref_list_fp' 119 --references-list '$temp_ref_list_fp'
99 #else if $assembly.ref.origin == 'silva' 120 #else if $assembly.ref.origin == 'silva'
100 --test-no-ref 121 --test-no-ref
101 --max-ref-num $assembly.ref.max_ref_num 122 --max-ref-num $assembly.ref.max_ref_num
102 #end if 123 #end if
103 #end if 124 $assembly.reuse_combined_alignments
104 125 #end if
105 --min-contig $min_contig 126
106 $split_scaffolds 127 --min-identity $assembly.min_identity
107 $large 128
129 --min-contig $min_contig
130 $split_scaffolds
131 $large
108 132
109 #if str($genes.gene_finding.tool) != 'none' 133 #if str($genes.gene_finding.tool) != 'none'
110 $genes.gene_finding.tool 134 $genes.gene_finding.tool
111 #if $genes.gene_finding.tool == '--gene_finding' or $genes.gene_finding.tool == '--glimmer' 135 #if $genes.gene_finding.tool == '--gene_finding' or $genes.gene_finding.tool == '--glimmer'
112 #set $gene_threshold = ','.join([x.strip() for x in str($genes.gene_finding.gene_thresholds).split(',')]) 136 #set $gene_threshold = ','.join([x.strip() for x in str($genes.gene_finding.gene_thresholds).split(',')])
113 --gene-thresholds '$gene_threshold' 137 --gene-thresholds '$gene_threshold'
114 #end if 138 #end if
115 #end if 139 #end if
116 140
117 $genes.rna_finding 141 $genes.rna_finding
118 $genes.conserved_genes_finding 142 $genes.conserved_genes_finding
119 $alignments.use_all_alignments 143 $alignments.use_all_alignments
120 --min-alignment $alignments.min_alignment 144 --min-alignment $alignments.min_alignment
121 --min-identity $alignments.min_identity 145 --ambiguity-usage '$alignments.ambiguity_usage'
122 --ambiguity-usage '$alignments.ambiguity_usage' 146 --ambiguity-score $alignments.ambiguity_score
123 --ambiguity-score $alignments.ambiguity_score 147 $alignments.fragmented
124 $alignments.fragmented 148 $alignments.upper_bound_assembly
125 $alignments.upper_bound_assembly
126 #if $alignments.upper_bound_min_con 149 #if $alignments.upper_bound_min_con
127 --upper-bound-min-con $alignments.upper_bound_min_con 150 --upper-bound-min-con $alignments.upper_bound_min_con
128 #end if 151 #end if
152 #if $alignments.local_mis_size
153 --local-mis-size $alignments.local_mis_size
154 #end if
129 155
130 #if $alignments.fragmented 156 #if $alignments.fragmented
131 #if $advanced.fragmented_max_indent != '' 157 #if $advanced.fragmented_max_indent != ''
132 --fragmented-max-indent $advanced.fragmented_max_indent 158 --fragmented-max-indent $advanced.fragmented_max_indent
133 #end if 159 #end if
134 #end if 160 #end if
135 161
136 #set $contig_thresholds = ','.join([x.strip() for x in str($advanced.contig_thresholds).split(',')]) 162 #set $contig_thresholds = ','.join([x.strip() for x in str($advanced.contig_thresholds).split(',')])
137 --contig-thresholds '$contig_thresholds' 163 --contig-thresholds '$contig_thresholds'
138 $advanced.strict_NA 164 $advanced.strict_NA
139 --extensive-mis-size $advanced.extensive_mis_size 165 --extensive-mis-size $advanced.extensive_mis_size
140 --scaffold-gap-max-size $advanced.scaffold_gap_max_size 166 --scaffold-gap-max-size $advanced.scaffold_gap_max_size
141 --unaligned-part-size $advanced.unaligned_part_size 167 --unaligned-part-size $advanced.unaligned_part_size
142 $advanced.skip_unaligned_mis_contigs 168 $advanced.skip_unaligned_mis_contigs
169 $advanced.report_all_metrics
170 --x-for-Nx $advanced.x_for_Nx
143 171
144 #if str($in.custom) == 'false' 172 #if str($in.custom) == 'false'
145 #for $k in $in.inputs 173 #for $k in $in.inputs
146 '$k' 174 '$k'
147 #end for 175 #end for
148 #else 176 #else
149 #for $k in $in.inputs 177 #for $k in $in.inputs
150 '$k.input' 178 '$k.input'
151 #end for 179 #end for
152 #end if 180 #end if
153 181 --threads \${GALAXY_SLOTS:-1}
154 --threads \${GALAXY_SLOTS:-1} 182
155 183 #if $assembly.type == 'genome'
156 && mkdir -p '$report_html.files_path' 184 && mkdir -p '$report_html.files_path'
157 && cp outputdir/*.html '$report_html.files_path' 185 && cp outputdir/*.html '$report_html.files_path'
158 186 #if $assembly.ref.use_ref
159 #if ($assembly.type == 'genome' and $assembly.ref.use_ref) or ($assembly.type == 'metagenome' and $assembly.ref.origin != 'none') 187 && cp -R outputdir/icarus_viewers '$report_html.files_path'
160 && cp -R outputdir/icarus_viewers '$report_html.files_path'
161 #end if
162
163 #if $assembly.type == 'metagenome'
164 && if [[ -d "outputdir/combined_reference/" ]]; then mkdir -p '$report_html_meta.files_path' && cp outputdir/combined_reference/*.html '$report_html_meta.files_path'; fi
165 #if $assembly.ref.origin != 'none'
166 && if [[ -d "outputdir/combined_reference/" ]]; then cp -R outputdir/combined_reference/icarus_viewers '$report_html_meta.files_path'; fi
167 && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p '$krona.files_path' && cp outputdir/krona_charts/*.html '$krona.files_path'; fi
168 #end if 188 #end if
169 #end if 189 #else
170 190 && if [[ -f "outputdir/report.tsv" ]]; then mkdir -p "outputdir/combined_reference/" && cp "outputdir/report.tsv" "outputdir/combined_reference/report.tsv"; fi
171 ]]> 191 && if [[ -f "outputdir/report.html" ]]; then mkdir -p "outputdir/combined_reference/" && cp outputdir/*.html "outputdir/combined_reference/"; fi
172 </command> 192 && mkdir -p '$report_html_meta.files_path'
193 && cp outputdir/combined_reference/*.html '$report_html_meta.files_path'
194 && if [[ -d "outputdir/icarus_viewers" ]]; then cp -R outputdir/icarus_viewers 'outputdir/combined_reference/'; fi
195 && if [[ -d "outputdir/combined_reference/icarus_viewers" ]]; then cp -R outputdir/combined_reference/icarus_viewers '$report_html_meta.files_path'; fi
196 && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p '$krona.files_path' && cp outputdir/krona_charts/*.html '$krona.files_path'; fi
197 #end if
198 ]]></command>
173 <inputs> 199 <inputs>
174 <conditional name="in"> 200 <conditional name="in">
175 <param name="custom" type="select" label="Use customized names for the input files?" help="They will be used in reports, plots and logs"> 201 <param name="custom" type="select" label="Use customized names for the input files?" help="They will be used in reports, plots and logs">
176 <option value="true">Yes, specify custom names</option> 202 <option value="true">Yes, specify custom names</option>
177 <option value="false" selected="true">No, use dataset names</option> 203 <option value="false" selected="true">No, use dataset names</option>
189 <conditional name="reads"> 215 <conditional name="reads">
190 <param name="reads_option" type="select" label="Reads options" help="Currently, the supported read types are Illumina unpaired, paired-end and mate-pair reads, PacBio SMRT, and Oxford Nanopore long reads."> 216 <param name="reads_option" type="select" label="Reads options" help="Currently, the supported read types are Illumina unpaired, paired-end and mate-pair reads, PacBio SMRT, and Oxford Nanopore long reads.">
191 <option value="disabled">Disabled</option> 217 <option value="disabled">Disabled</option>
192 <option value="single">Illumina single-end reads</option> 218 <option value="single">Illumina single-end reads</option>
193 <option value="paired">Illumina paired-end reads</option> 219 <option value="paired">Illumina paired-end reads</option>
220 <option value="paired_collection">Illumina paired-end reads in paired collection</option>
194 <option value="paired_interlaced">Illumina interlaced paired-end reads</option> 221 <option value="paired_interlaced">Illumina interlaced paired-end reads</option>
195 <option value="mate_paired">Illumina mate-pair reads</option> 222 <option value="mate_paired">Illumina mate-pair reads</option>
196 <option value="pacbio">Pacbio SMRT reads</option> 223 <option value="pacbio">Pacbio SMRT reads</option>
197 <option value="nanopore">Nanopore reads</option> 224 <option value="nanopore">Nanopore reads</option>
198 </param> 225 </param>
202 </when> 229 </when>
203 <when value="paired"> 230 <when value="paired">
204 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" /> 231 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
205 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" /> 232 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
206 </when> 233 </when>
207 234 <when value="paired_collection">
235 <param name="input_1" type="data_collection" collection_type="paired" format="fastq,fastq.gz,fasta,fasta.gz" label="FASTQ/FASTA files" />
236 </when>
208 <when value="paired_interlaced"> 237 <when value="paired_interlaced">
209 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" /> 238 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
210 </when> 239 </when>
211 <when value="mate_paired"> 240 <when value="mate_paired">
212 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" /> 241 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
253 <param name="orga_type" type="select" label="Type of organism"> 282 <param name="orga_type" type="select" label="Type of organism">
254 <option value="">Prokaryotes: use of GeneMarkS for gene finding (default)</option> 283 <option value="">Prokaryotes: use of GeneMarkS for gene finding (default)</option>
255 <option value="--eukaryote">Eukaryote: use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding (--eukaryote)</option> 284 <option value="--eukaryote">Eukaryote: use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding (--eukaryote)</option>
256 <option value="--fungus">Fungus: use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding (--fungus)</option> 285 <option value="--fungus">Fungus: use of GeneMark-ES for gene finding, Barrnap for ribosomal RNA genes prediction, BUSCO for conserved orthologs finding (--fungus)</option>
257 </param> 286 </param>
287 <expand macro="min_identity_macros" value="95"/>
258 </when> 288 </when>
259 <when value="metagenome"> 289 <when value="metagenome">
260 <conditional name="ref"> 290 <conditional name="ref">
261 <param name="origin" type="select" label="Reference genome" help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference."> 291 <param name="origin" type="select" label="Reference genome" help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference.">
262 <option value="history">From history</option> 292 <option value="history">From history</option>
273 <when value="silva"> 303 <when value="silva">
274 <param name="max_ref_num" argument="-max-ref-num" type="integer" value="50" label="Maximum number of reference genomes (per each assembly) to download after searching in the SILVA databa" /> 304 <param name="max_ref_num" argument="-max-ref-num" type="integer" value="50" label="Maximum number of reference genomes (per each assembly) to download after searching in the SILVA databa" />
275 </when> 305 </when>
276 <when value="none"/> 306 <when value="none"/>
277 </conditional> 307 </conditional>
308 <param argument="--reuse-combined-alignments" type="boolean" truevalue="--reuse-combined-alignments" falsevalue="" checked="false" label="Reuse the alignments on the combined reference" help="Reuse the alignments on the combined reference in the subsequent runs per separate references. That is, the alignment procedure is performed only once (for all assemblies against the combined reference) and does NOT executed for each subgroups of contigs against the corresponding separate reference genomes. In each separate reference run, all precomputed assembly alignments for other references are simply ignored" />
309 <expand macro="min_identity_macros" value="90"/>
278 </when> 310 </when>
279 </conditional> 311 </conditional>
280 <param argument="--min-contig" type="integer" value="500" label="Lower threshold for a contig length (in bp)" help="Shorter contigs won't be taken into account"/> 312 <param argument="--min-contig" type="integer" value="500" label="Lower threshold for a contig length (in bp)" help="Shorter contigs won't be taken into account"/>
281 <param argument="--split-scaffolds" type="boolean" truevalue="--split-scaffolds" falsevalue="" checked="false" label="Are assemblies scaffolds rather than contigs?" help="QUAST will add split versions of assemblies to the comparison. Assemblies are split by continuous fragments of N's of length >= 10. If broken version is equal to the original assembly (i.e. nothing was split) it is not included in the comparison."/> 313 <param argument="--split-scaffolds" type="boolean" truevalue="--split-scaffolds" falsevalue="" checked="false" label="Are assemblies scaffolds rather than contigs?" help="QUAST will add split versions of assemblies to the comparison. Assemblies are split by continuous fragments of N's of length >= 10. If broken version is equal to the original assembly (i.e. nothing was split) it is not included in the comparison."/>
282 <param argument="--large" type="boolean" truevalue="--large" falsevalue="" checked="false" label="Is genome large (> 100 Mbp)?" help="Use optimal parameters for evaluation of large genomes. Affects speed and accuracy. In particular, imposes --eukaryote --min-contig 3000 --min-alignment 500 --extensive-mis-size 7000 (can be overridden manually with the corresponding options). In addition, this mode tries to identify misassemblies caused by transposable elements and exclude them from the number of misassemblies."/> 314 <param argument="--large" type="boolean" truevalue="--large" falsevalue="" checked="false" label="Is genome large (> 100 Mbp)?" help="Use optimal parameters for evaluation of large genomes. Affects speed and accuracy. In particular, imposes --eukaryote --min-contig 3000 --min-alignment 500 --extensive-mis-size 7000 (can be overridden manually with the corresponding options). In addition, this mode tries to identify misassemblies caused by transposable elements and exclude them from the number of misassemblies."/>
301 <param argument="--conserved-genes-finding" type="boolean" truevalue="--conserved-genes-finding" falsevalue="" checked="false" label="Enables search for Universal Single-Copy Orthologs using BUSCO?" help="By default, we assume that the genome is prokaryotic, and BUSCO uses the bacterial database of orthologs. If the genome is eukaryotic (fungal), use --eukaryote (--fungus) option to force BUSCO to work with the eukaryotic (fungal) database. "/> 333 <param argument="--conserved-genes-finding" type="boolean" truevalue="--conserved-genes-finding" falsevalue="" checked="false" label="Enables search for Universal Single-Copy Orthologs using BUSCO?" help="By default, we assume that the genome is prokaryotic, and BUSCO uses the bacterial database of orthologs. If the genome is eukaryotic (fungal), use --eukaryote (--fungus) option to force BUSCO to work with the eukaryotic (fungal) database. "/>
302 </section> 334 </section>
303 <section name="alignments" title="Alignments"> 335 <section name="alignments" title="Alignments">
304 <param argument="--use-all-alignments" type="boolean" truevalue="--use-all-alignments" falsevalue="" checked="false" label="Use all alignments as in QUAST v.1.*. to compute genome fraction, # genomic features, # operons metrics?" help="By default, QUAST v.2.0 and higher filters out ambiguous and redundant alignments, keeping only one alignment per contig (or one set of non-overlapping or slightly overlapping alignments)"/> 336 <param argument="--use-all-alignments" type="boolean" truevalue="--use-all-alignments" falsevalue="" checked="false" label="Use all alignments as in QUAST v.1.*. to compute genome fraction, # genomic features, # operons metrics?" help="By default, QUAST v.2.0 and higher filters out ambiguous and redundant alignments, keeping only one alignment per contig (or one set of non-overlapping or slightly overlapping alignments)"/>
305 <param argument="--min-alignment" type="integer" value="65" label="Minimum length of alignment" help="Alignments shorter than this value will be filtered. Note that all alignments shorter than 65 bp will be filtered regardless of this threshold."/> 337 <param argument="--min-alignment" type="integer" value="65" label="Minimum length of alignment" help="Alignments shorter than this value will be filtered. Note that all alignments shorter than 65 bp will be filtered regardless of this threshold."/>
306 <param argument="--min-identity" type="float" value="95.0" label="Minimum IDY% considered as proper alignment" help="Alignments with IDY% worse than this value will be filtered. ote that all alignments with IDY% less than 80.0% will be filtered regardless of this threshold. "/>
307 <param argument="--ambiguity-usage" type="select" label="How processing equally good alignments of a contig (probably repeats)?" help=""> 338 <param argument="--ambiguity-usage" type="select" label="How processing equally good alignments of a contig (probably repeats)?" help="">
308 <option value="none">Skip all such alignments</option> 339 <option value="none">Skip all such alignments</option>
309 <option value="one" selected="true">Take only one (the very best one)</option> 340 <option value="one" selected="true">Take only one (the very best one)</option>
310 <option value="all">Use all alignments. It can cause a significant increase of # mismatches (repeats are almost always inexact due to accumulated SNPs, indels, etc.). It is useful for metagenomic assemblies where ambiguous alignments might represent homologous sequences of different strains</option> 341 <option value="all">Use all alignments. It can cause a significant increase of # mismatches (repeats are almost always inexact due to accumulated SNPs, indels, etc.). It is useful for metagenomic assemblies where ambiguous alignments might represent homologous sequences of different strains</option>
311 </param> 342 </param>
312 <param argument="--ambiguity-score" type="float" value="0.99" min="0.8" max="1.0" label="Score S for defining equally good alignments of a single contig" help="All alignments are sorted by decreasing LEN × IDY% value. All alignments with LEN × IDY% less than S × best(LEN × IDY%) are discarded. "/> 343 <param argument="--ambiguity-score" type="float" value="0.99" min="0.8" max="1.0" label="Score S for defining equally good alignments of a single contig" help="All alignments are sorted by decreasing LEN × IDY% value. All alignments with LEN × IDY% less than S × best(LEN × IDY%) are discarded. "/>
313 <param argument="--fragmented" type="boolean" truevalue="--fragmented" falsevalue="" checked="false" label="Fragmented reference genome" help="Reference genome is fragmented (e.g. a scaffold reference). QUAST will try to detect misassemblies caused by the fragmentation and mark them fake (will be excluded from misassemblies). Note: QUAST will not detect misassemblies caused by the linear representation of circular genome "/> 344 <param argument="--fragmented" type="boolean" truevalue="--fragmented" falsevalue="" checked="false" label="Fragmented reference genome" help="Reference genome is fragmented (e.g. a scaffold reference). QUAST will try to detect misassemblies caused by the fragmentation and mark them fake (will be excluded from misassemblies). Note: QUAST will not detect misassemblies caused by the linear representation of circular genome "/>
314 <param argument="--upper-bound-assembly" type="boolean" truevalue="--upper-bound-assembly" falsevalue="" label="Simulate upper bound assembly" help="Simulate upper bound assembly based on the reference genome and a given set reads (mate-pairs or long reads, such as Pacbio SMRT/Oxford Nanopore, are REQUIRED). This assembly is added to the comparison and could be useful for estimating the upper bounds of completeness and contiguity that theoretically can be reached by assembly software from this particular set of reads. The concept is based on the fact that the reference genome cannot be completely reconstructed from raw reads due to long genomic repeats and low covered regions." /> 345 <param argument="--upper-bound-assembly" type="boolean" truevalue="--upper-bound-assembly" falsevalue="" label="Simulate upper bound assembly" help="Simulate upper bound assembly based on the reference genome and a given set reads (mate-pairs or long reads, such as Pacbio SMRT/Oxford Nanopore, are REQUIRED). This assembly is added to the comparison and could be useful for estimating the upper bounds of completeness and contiguity that theoretically can be reached by assembly software from this particular set of reads. The concept is based on the fact that the reference genome cannot be completely reconstructed from raw reads due to long genomic repeats and low covered regions." />
315 <param argument="--upper-bound-min-con" type="integer" value="" optional="true" label="Minimal number of 'connecting reads' needed for joining upper bound contigs into a scaffold" help="This is important for a realistic estimation of genome assembly fragmentation due to long repeats. The default values is 2 for mate-pairs and 1 for long reads (PacBio or Nanopore libraries)"/> 346 <param argument="--upper-bound-min-con" type="integer" value="" optional="true" label="Minimal number of 'connecting reads' needed for joining upper bound contigs into a scaffold" help="This is important for a realistic estimation of genome assembly fragmentation due to long repeats. The default values is 2 for mate-pairs and 1 for long reads (PacBio or Nanopore libraries)"/>
347 <param argument="--local-mis-size" type="integer" value="200" optional="true" label="Minimal local misassembly size" help="Lower threshold for the local misassembly size. Shorter inconsistencies are considered as (long) indels. The default value is 200 bp. Note that the threshold should be equal to or lower than minimal extensive misassembly size, which is 1000 bp by default"/>
316 </section> 348 </section>
317 <section name="advanced" title="Advanced options"> 349 <section name="advanced" title="Advanced options">
318 <param argument="--contig-thresholds" type="text" value="0,1000" label="Comma-separated list of contig length thresholds (in bp)" help="Used in # contigs ≥ x and total length (≥ x) metrics"/> 350 <param argument="--contig-thresholds" type="text" value="0,1000" label="Comma-separated list of contig length thresholds (in bp)" help="Used in # contigs ≥ x and total length (≥ x) metrics"/>
319 <param argument="--strict-NA" type="boolean" truevalue="--strict-NA" falsevalue="" checked="false" label="Break contigs at every misassembly event (including local ones) to compute NAx and NGAx statistics?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/> 351 <param argument="--strict-NA" type="boolean" truevalue="--strict-NA" falsevalue="" checked="false" label="Break contigs at every misassembly event (including local ones) to compute NAx and NGAx statistics?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/>
320 <param argument="--extensive-mis-size" type="integer" value="1000" min="85" label="Lower threshold for the relocation size (gap or overlap size between left and right flanking sequence)" help="Shorter relocations are considered as local misassemblies. It does not affect other types of extensive misassemblies (inversions and translocations). The default value is 1000 bp. Note that the threshold should be greater than maximum indel length which is 85 bp."/> 352 <param argument="--extensive-mis-size" type="integer" value="1000" min="85" label="Lower threshold for the relocation size (gap or overlap size between left and right flanking sequence)" help="Shorter relocations are considered as local misassemblies. It does not affect other types of extensive misassemblies (inversions and translocations). The default value is 1000 bp. Note that the threshold should be greater than maximum indel length which is 85 bp."/>
321 <param argument="--scaffold-gap-max-size" type="integer" value="1000" label="Max allowed scaffold gap length difference for detecting corresponding type of misassemblies" help="Longer inconsistencies are considered as relocations and thus, counted as extensive misassemblies. The default value is 10000 bp. Note that the threshold make sense only if it is greater than extensive misassembly size"/> 353 <param argument="--scaffold-gap-max-size" type="integer" value="1000" label="Max allowed scaffold gap length difference for detecting corresponding type of misassemblies" help="Longer inconsistencies are considered as relocations and thus, counted as extensive misassemblies. The default value is 10000 bp. Note that the threshold make sense only if it is greater than extensive misassembly size"/>
322 <param argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/> 354 <param argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/>
323 <param argument="--skip-unaligned-mis-contigs" type="boolean" truevalue="" falsevalue="--skip-unaligned-mis-contigs" checked="true" label="Distinguish contigs with more than 50% unaligned bases as a separate group of contigs?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/> 355 <param argument="--skip-unaligned-mis-contigs" type="boolean" truevalue="" falsevalue="--skip-unaligned-mis-contigs" checked="true" label="Distinguish contigs with more than 50% unaligned bases as a separate group of contigs?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/>
324 <param argument="--fragmented-max-indent" type="integer" min="0" value="" optional="true" label="Fragment max indent" help="Mark translocation as fake if both alignments are located no further than N bases from the ends of the reference fragments. The value should be less than extensive misassembly size.Default value is 50. Note: requires --fragmented option" /> 356 <param argument="--fragmented-max-indent" type="integer" min="0" value="" optional="true" label="Fragment max indent" help="Mark translocation as fake if both alignments are located no further than N bases from the ends of the reference fragments. The value should be less than extensive misassembly size.Default value is 50. Note: requires --fragmented option" />
357 <param argument="--report-all-metrics" type="boolean" truevalue="--report-all-metrics" falsevalue="" checked="false" label="Report all metrics" help="Keep all quality metrics in the main report. Usually, all not-relevant metrics are not included in the report, e.g., reference-based metrics in the no-reference mode. Also, if metric values are undefined for all input assemblies, the metric is removed from the report" />
358 <param argument="--x-for-Nx" type="integer" min="0" max="100" value="90" label="Report Nx, Lx, etc metrics for specific value of 'x'" help="Value of 'x' for Nx, Lx, NGx, NGAx, etc metrics reported in addition to N50, L50, NG50, NGA50, etc" />
325 </section> 359 </section>
326 <param name="output_files" type="select" display="checkboxes" optional="true" multiple="true" label="Output files"> 360 <param name="output_files" type="select" display="checkboxes" optional="true" multiple="true" label="Output files">
327 <option value="html" selected="true">HTML reports</option> 361 <option value="html" selected="true">HTML reports</option>
328 <option value="pdf">PDF reports</option> 362 <option value="pdf">PDF reports</option>
329 <option value="tabular">Tabular reports</option> 363 <option value="tabular">Tabular reports</option>
338 </data> 372 </data>
339 <data name="report_tabular_meta" format="tabular" label="${tool.name} on ${on_string}: tabular report for combined reference genome" from_work_dir="outputdir/combined_reference/report.tsv"> 373 <data name="report_tabular_meta" format="tabular" label="${tool.name} on ${on_string}: tabular report for combined reference genome" from_work_dir="outputdir/combined_reference/report.tsv">
340 <filter>assembly['type'] == 'metagenome' and 'tabular' in output_files</filter> 374 <filter>assembly['type'] == 'metagenome' and 'tabular' in output_files</filter>
341 </data> 375 </data>
342 <data name="report_html" format="html" label="${tool.name} on ${on_string}: HTML report" from_work_dir="outputdir/report.html"> 376 <data name="report_html" format="html" label="${tool.name} on ${on_string}: HTML report" from_work_dir="outputdir/report.html">
343 <filter>'html' in output_files</filter> 377 <filter>assembly['type'] == 'genome' and 'html' in output_files</filter>
344 </data> 378 </data>
345 <data name="report_html_meta" format="html" label="${tool.name} on ${on_string}: HTML report for combined reference genome" from_work_dir="outputdir/combined_reference/report.html"> 379 <data name="report_html_meta" format="html" label="${tool.name} on ${on_string}: HTML report for combined reference genome" from_work_dir="outputdir/combined_reference/report.html">
346 <filter>assembly['type'] == 'metagenome' and 'html' in output_files</filter> 380 <filter>assembly['type'] == 'metagenome' and 'html' in output_files</filter>
347 </data> 381 </data>
348 <data name="report_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF report" from_work_dir="outputdir/report.pdf"> 382 <data name="report_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF report" from_work_dir="outputdir/report.pdf">
417 <param name="tool" value="--gene_finding"/> 451 <param name="tool" value="--gene_finding"/>
418 <param name="gene_thresholds" value="0,300,1500,3000"/> 452 <param name="gene_thresholds" value="0,300,1500,3000"/>
419 </conditional> 453 </conditional>
420 <param name="rna_finding" value="true"/> 454 <param name="rna_finding" value="true"/>
421 <param name="conserved_genes_finding" value="true"/> 455 <param name="conserved_genes_finding" value="true"/>
456 <param name="min_identity" value="95.0"/>
422 </section> 457 </section>
423 <section name="alignments"> 458 <section name="alignments">
424 <param name="use_all_alignments" value="true"/> 459 <param name="use_all_alignments" value="true"/>
425 <param name="min_alignment" value="65"/> 460 <param name="min_alignment" value="65"/>
426 <param name="min_identity" value="95.0"/>
427 <param name="ambiguity_usage" value="one"/> 461 <param name="ambiguity_usage" value="one"/>
428 <param name="ambiguity_score" value="0.99"/> 462 <param name="ambiguity_score" value="0.99"/>
429 </section> 463 </section>
430 <section name="advanced"> 464 <section name="advanced">
431 <param name="contig_thresholds" value="0,1000"/> 465 <param name="contig_thresholds" value="0,1000"/>
487 <param name="type" value="genome"/> 521 <param name="type" value="genome"/>
488 <conditional name="ref"> 522 <conditional name="ref">
489 <param name="use_ref" value="false"/> 523 <param name="use_ref" value="false"/>
490 </conditional> 524 </conditional>
491 <param name="orga_type" value="--eukaryote"/> 525 <param name="orga_type" value="--eukaryote"/>
526 <param name="min_identity" value="95.0"/>
492 </conditional> 527 </conditional>
493 <param name="min_contig" value="500"/> 528 <param name="min_contig" value="500"/>
494 <param name="split_scaffolds" value="false"/> 529 <param name="split_scaffolds" value="false"/>
495 <param name="large" value="false"/> 530 <param name="large" value="false"/>
496 <section name="genes"> 531 <section name="genes">
497 <conditional name="gene_finding"> 532 <conditional name="gene_finding">
498 <param name="tool" value="none"/> 533 <param name="tool" value="none"/>
534 </conditional>
535 <param name="rna_finding" value="false"/>
536 <param name="conserved_genes_finding" value="false"/>
537 </section>
538 <section name="alignments">
539 <param name="use_all_alignments" value="false"/>
540 <param name="min_alignment" value="65"/>
541 <param name="ambiguity_usage" value="one"/>
542 <param name="ambiguity_score" value="0.99"/>
543 <param name="fragmented" value="false"/>
544 </section>
545 <section name="advanced">
546 <param name="contig_thresholds" value="0,1000, 500"/>
547 <param name="strict_NA" value="false"/>
548 <param name="extensive_mis_size" value="1000"/>
549 <param name="scaffold_gap_max_size" value="1000"/>
550 <param name="unaligned_part_size" value="500"/>
551 <param name="skip_unaligned_mis_contigs" value="-"/>
552 </section>
553 <param name="output_files" value="html,pdf,log" />
554 <output name="log" file="test3.log" ftype="txt" compare="sim_size"/>
555 <output name="report_html" file="test3_report.html" compare="sim_size"/>
556 <output name="report_pdf" file="test3_report.pdf" compare="sim_size"/>
557 </test>
558 <!-- Test 04: metagenomics -->
559 <test expect_num_outputs="3">
560 <conditional name="in">
561 <param name="custom" value="false"/>
562 <param name="inputs" value="contigs3.fasta"/>
563 </conditional>
564 <conditional name="assembly">
565 <param name="type" value="metagenome"/>
566 <conditional name="ref">
567 <param name="origin" value="none"/>
568 </conditional>
569 </conditional>
570 <param name="min_contig" value="500"/>
571 <param name="split_scaffolds" value="false"/>
572 <param name="large" value="false"/>
573 <section name="genes">
574 <conditional name="gene_finding">
575 <param name="tool" value="--mgm"/>
499 </conditional> 576 </conditional>
500 <param name="rna_finding" value="false"/> 577 <param name="rna_finding" value="false"/>
501 <param name="conserved_genes_finding" value="false"/> 578 <param name="conserved_genes_finding" value="false"/>
502 </section> 579 </section>
503 <section name="alignments"> 580 <section name="alignments">
514 <param name="extensive_mis_size" value="1000"/> 591 <param name="extensive_mis_size" value="1000"/>
515 <param name="scaffold_gap_max_size" value="1000"/> 592 <param name="scaffold_gap_max_size" value="1000"/>
516 <param name="unaligned_part_size" value="500"/> 593 <param name="unaligned_part_size" value="500"/>
517 <param name="skip_unaligned_mis_contigs" value="-"/> 594 <param name="skip_unaligned_mis_contigs" value="-"/>
518 </section> 595 </section>
519 <param name="output_files" value="html,pdf,log" /> 596 <param name="output_files" value="log,html,tabular"/>
520 <output name="log" file="test3.log" ftype="txt" compare="sim_size"/>
521 <output name="report_html" file="test3_report.html" compare="sim_size"/>
522 <output name="report_pdf" file="test3_report.pdf" compare="sim_size"/>
523 </test>
524 <!-- Test 04: metagenomics -->
525 <test>
526 <conditional name="in">
527 <param name="custom" value="false"/>
528 <param name="inputs" value="contigs3.fasta"/>
529 </conditional>
530 <conditional name="assembly">
531 <param name="type" value="metagenome"/>
532 <conditional name="ref">
533 <param name="origin" value="none"/>
534 </conditional>
535 </conditional>
536 <param name="min_contig" value="500"/>
537 <param name="split_scaffolds" value="false"/>
538 <param name="large" value="false"/>
539 <section name="genes">
540 <conditional name="gene_finding">
541 <param name="tool" value="--mgm"/>
542 </conditional>
543 <param name="rna_finding" value="false"/>
544 <param name="conserved_genes_finding" value="false"/>
545 </section>
546 <section name="alignments">
547 <param name="use_all_alignments" value="false"/>
548 <param name="min_alignment" value="65"/>
549 <param name="min_identity" value="95.0"/>
550 <param name="ambiguity_usage" value="one"/>
551 <param name="ambiguity_score" value="0.99"/>
552 <param name="fragmented" value="false"/>
553 </section>
554 <section name="advanced">
555 <param name="contig_thresholds" value="0,1000, 500"/>
556 <param name="strict_NA" value="false"/>
557 <param name="extensive_mis_size" value="1000"/>
558 <param name="scaffold_gap_max_size" value="1000"/>
559 <param name="unaligned_part_size" value="500"/>
560 <param name="skip_unaligned_mis_contigs" value="-"/>
561 </section>
562 <param name="output_files" value="log"/>
563 <output name="log_meta" ftype="txt"> 597 <output name="log_meta" ftype="txt">
564 <assert_contents> 598 <assert_contents>
565 <has_text text="Reference genomes are not found" /> 599 <has_text text="Reference genomes are not found" />
566 </assert_contents> 600 </assert_contents>
567 </output> 601 </output>
602 <output name="report_tabular_meta" ftype="tabular">
603 <assert_contents>
604 <has_text text="# contigs (>= 0 bp)"/>
605 <has_text text="contigs3_fasta"/>
606 <has_text text="# N's per 100 kbp"/>
607 <has_n_lines n="17"/>
608 </assert_contents>
609 </output>
610 <output name="report_html_meta" ftype="html">
611 <assert_contents>
612 <has_text text="Quality Assessment Tool for Genome Assemblies" />
613 <has_text text="contigs3_fasta" />
614 <has_text text="Statistics without reference" />
615 </assert_contents>
616 </output>
568 </test> 617 </test>
569 <!-- Test 05: FASTQ read files --> 618 <!-- Test 05: FASTQ read files -->
570 <test expect_num_outputs="3"> 619 <test expect_num_outputs="3">
571 <conditional name="in"> 620 <conditional name="in">
572 <param name="custom" value="true"/> 621 <param name="custom" value="true"/>
594 <param name="upper_bound_assembly" value="true"/> 643 <param name="upper_bound_assembly" value="true"/>
595 <param name="upper_bound_min_con" value="1"/> 644 <param name="upper_bound_min_con" value="1"/>
596 </section> 645 </section>
597 <param name="output_files" value="tabular"/> 646 <param name="output_files" value="tabular"/>
598 <output name="report_tabular" file="test5.tab" ftype="tabular"/> 647 <output name="report_tabular" file="test5.tab" ftype="tabular"/>
599 <output name="mis_ass" file="test5_missasemblies.tab" ftype="tabular"/> 648 <output name="mis_ass" ftype="tabular">
600 <output name="unalign" file="test5_unaligned.tab" ftype="tabular"/> 649 <assert_contents>
650 <has_text text="All statistics are based on contigs of size >= 500 bp"/>
651 <has_text text="# scaffold misassemblies"/>
652 <has_text text="contig1"/>
653 </assert_contents>
654 </output>
655 <output name="unalign" ftype="tabular">
656 <assert_contents>
657 <has_text text="Fully unaligned length"/>
658 <has_text text="contig1"/>
659 </assert_contents>
660 </output>
601 </test> 661 </test>
602 <!-- Test 06: FASTQ.gz read files --> 662 <!-- Test 06: FASTQ.gz read files -->
603 <test expect_num_outputs="1"> 663 <test expect_num_outputs="1">
604 <conditional name="in"> 664 <conditional name="in">
605 <param name="custom" value="true"/> 665 <param name="custom" value="true"/>
640 <output name="report_tabular" file="test7.tab" ftype="tabular"/> 700 <output name="report_tabular" file="test7.tab" ftype="tabular"/>
641 </test> 701 </test>
642 <!-- Test 08: metagenomics all tab outputs--> 702 <!-- Test 08: metagenomics all tab outputs-->
643 <test expect_num_outputs="3"> 703 <test expect_num_outputs="3">
644 <conditional name="in"> 704 <conditional name="in">
645 <param name="custom" value="false"/> 705 <repeat name="inputs">
646 <param name="inputs" value="test8.fasta"/> 706 <param name="input" value="meta_contigs_1.fasta"/>
707 <param name="labels" value="meta_contigs_1"/>
708 </repeat>
709 <repeat name="inputs">
710 <param name="input" value="meta_contigs_2.fasta"/>
711 <param name="labels" value="meta_contigs_2"/>
712 </repeat>
647 </conditional> 713 </conditional>
648 <conditional name="assembly"> 714 <conditional name="assembly">
649 <param name="type" value="metagenome"/> 715 <param name="type" value="metagenome"/>
650 <conditional name="ref"> 716 <conditional name="ref">
651 <param name="origin" value="none"/> 717 <param name="origin" value="history"/>
652 </conditional> 718 <param name="r" value="meta_ref_1.fasta,meta_ref_2.fasta,meta_ref_3.fasta"/>
719 </conditional>
720 <param name="min_identity" value="95.0"/>
653 </conditional> 721 </conditional>
654 <param name="min_contig" value="500"/> 722 <param name="min_contig" value="500"/>
655 <param name="split_scaffolds" value="false"/> 723 <param name="split_scaffolds" value="false"/>
656 <param name="large" value="false"/> 724 <param name="large" value="false"/>
657 <section name="genes"> 725 <section name="genes">
662 <param name="conserved_genes_finding" value="false"/> 730 <param name="conserved_genes_finding" value="false"/>
663 </section> 731 </section>
664 <section name="alignments"> 732 <section name="alignments">
665 <param name="use_all_alignments" value="false"/> 733 <param name="use_all_alignments" value="false"/>
666 <param name="min_alignment" value="65"/> 734 <param name="min_alignment" value="65"/>
667 <param name="min_identity" value="95.0"/>
668 <param name="ambiguity_usage" value="one"/> 735 <param name="ambiguity_usage" value="one"/>
669 <param name="ambiguity_score" value="0.99"/> 736 <param name="ambiguity_score" value="0.99"/>
670 <param name="fragmented" value="false"/> 737 <param name="fragmented" value="false"/>
671 </section> 738 </section>
672 <section name="advanced"> 739 <section name="advanced">
678 <param name="skip_unaligned_mis_contigs" value="-"/> 745 <param name="skip_unaligned_mis_contigs" value="-"/>
679 </section> 746 </section>
680 <param name="output_files" value="tabular,summary"/> 747 <param name="output_files" value="tabular,summary"/>
681 <output name="report_tabular_meta" ftype="tabular"> 748 <output name="report_tabular_meta" ftype="tabular">
682 <assert_contents> 749 <assert_contents>
683 <has_text text="contigs (>= 0 bp)" /> 750 <has_text text="# contigs (>= 0 bp)"/>
751 <has_text text="meta_ref_3_fasta"/>
752 <has_text text="# N's per 100 kbp"/>
753 <has_n_lines n="34"/>
684 </assert_contents> 754 </assert_contents>
685 </output> 755 </output>
686 <output_collection name="metrics_tabular" type="list" count="14"/> 756 <output_collection name="metrics_tabular" type="list" count="15"/>
687 <output_collection name="metrics_pdf" type="list" count="15"/> 757 <output_collection name="metrics_pdf" type="list" count="16"/>
688 </test> 758 </test>
689 <!-- Test 09: metagenomics log, html and krona outputs--> 759 <!-- Test 09: metagenomics log, html and krona outputs-->
690 <test expect_num_outputs="4"> 760 <test expect_num_outputs="2">
691 <conditional name="in"> 761 <conditional name="in">
692 <param name="custom" value="false"/> 762 <repeat name="inputs">
693 <param name="inputs" value="test8.fasta"/> 763 <param name="input" value="meta_contigs_1.fasta"/>
764 <param name="labels" value="meta_contigs_1"/>
765 </repeat>
766 <repeat name="inputs">
767 <param name="input" value="meta_contigs_2.fasta"/>
768 <param name="labels" value="meta_contigs_2"/>
769 </repeat>
694 </conditional> 770 </conditional>
695 <conditional name="assembly"> 771 <conditional name="assembly">
696 <param name="type" value="metagenome"/> 772 <param name="type" value="metagenome"/>
697 <conditional name="ref"> 773 <conditional name="ref">
698 <param name="origin" value="none"/> 774 <param name="origin" value="list"/>
699 </conditional> 775 <param name="references_list" value="Lactobacillus_delbrueckii_bulgaricus,Lactobacillus_reuteri"/>
776 </conditional>
777 <param name="min_identity" value="95.0"/>
700 </conditional> 778 </conditional>
701 <param name="min_contig" value="500"/> 779 <param name="min_contig" value="500"/>
702 <param name="split_scaffolds" value="false"/> 780 <param name="split_scaffolds" value="false"/>
703 <param name="large" value="false"/> 781 <param name="large" value="false"/>
704 <section name="genes"> 782 <section name="genes">
709 <param name="conserved_genes_finding" value="false"/> 787 <param name="conserved_genes_finding" value="false"/>
710 </section> 788 </section>
711 <section name="alignments"> 789 <section name="alignments">
712 <param name="use_all_alignments" value="false"/> 790 <param name="use_all_alignments" value="false"/>
713 <param name="min_alignment" value="65"/> 791 <param name="min_alignment" value="65"/>
714 <param name="min_identity" value="95.0"/>
715 <param name="ambiguity_usage" value="all"/> 792 <param name="ambiguity_usage" value="all"/>
716 <param name="ambiguity_score" value="0.99"/> 793 <param name="ambiguity_score" value="0.99"/>
717 <param name="fragmented" value="false"/> 794 <param name="fragmented" value="false"/>
718 </section> 795 </section>
719 <section name="advanced"> 796 <section name="advanced">
722 <param name="extensive_mis_size" value="1000"/> 799 <param name="extensive_mis_size" value="1000"/>
723 <param name="scaffold_gap_max_size" value="1000"/> 800 <param name="scaffold_gap_max_size" value="1000"/>
724 <param name="unaligned_part_size" value="500"/> 801 <param name="unaligned_part_size" value="500"/>
725 <param name="skip_unaligned_mis_contigs" value="-"/> 802 <param name="skip_unaligned_mis_contigs" value="-"/>
726 </section> 803 </section>
727 <param name="output_files" value="html,log,krona"/> 804 <param name="output_files" value="html,log"/>
728 <output name="report_html" ftype="html"> 805 <output name="report_html_meta" ftype="html">
729 <assert_contents> 806 <assert_contents>
730 <has_text text="Vibrio_parahaemolyticus" /> 807 <has_text text="meta_contigs_2_fasta" />
731 </assert_contents> 808 <has_text text="combined_reference" />
732 </output> 809 <has_text text="Lactobacillus" />
733 <output name="report_html_meta" ftype="html">
734 <assert_contents>
735 <has_text text="Total length (>= 1000 bp)" />
736 </assert_contents> 810 </assert_contents>
737 </output> 811 </output>
738 <output name="log_meta" ftype="txt"> 812 <output name="log_meta" ftype="txt">
739 <assert_contents> 813 <assert_contents>
740 <has_text text="Vibrio_parahaemolyticus | successfully downloaded" /> 814 <has_text text="List of references was provided, starting to download reference genomes from NCBI" />
815 <has_text text="Lactobacillus_delbrueckii_bulgaricus" />
741 </assert_contents> 816 </assert_contents>
742 </output> 817 </output>
743 <output name="krona" ftype="html"> 818 </test>
819 <!-- Test 10: Test new options -->
820 <test expect_num_outputs="1">
821 <conditional name="in">
822 <param name="custom" value="true"/>
823 <repeat name="inputs">
824 <param name="input" value="contigs1.fna"/>
825 <param name="labels" value="contig1"/>
826 </repeat>
827 <repeat name="inputs">
828 <param name="input" value="contigs2.fna"/>
829 <param name="labels" value="contig2"/>
830 </repeat>
831 </conditional>
832 <section name="alignments">
833 <param name="local_mis_size" value="210"/>
834 </section>
835 <conditional name="assembly">
836 <param name="type" value="genome"/>
837 <conditional name="ref">
838 <param name="use_ref" value="false"/>
839 </conditional>
840 </conditional>
841 <section name="advanced">
842 <param name="report_all_metrics" value="true"/>
843 <param name="x_for_Nx" value="80"/>
844 </section>
845 <param name="output_files" value="tabular"/>
846 <output name="report_tabular" file="test10_tabular_report.tab" ftype="tabular"/>
847 </test>
848 <!-- Test 11: Test paired fastq.gz inputs -->
849 <test expect_num_outputs="1">
850 <conditional name="in">
851 <param name="custom" value="true"/>
852 <repeat name="inputs">
853 <param name="input" value="contigs1.fna"/>
854 <param name="labels" value="contig1"/>
855 </repeat>
856 </conditional>
857 <conditional name="reads">
858 <param name="reads_option" value="paired"/>
859 <param name="input_1" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
860 <param name="input_2" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
861 </conditional>
862 <conditional name="assembly">
863 <param name="type" value="genome"/>
864 <conditional name="ref">
865 <param name="use_ref" value="false"/>
866 </conditional>
867 </conditional>
868 <param name="output_files" value="tabular"/>
869 <output name="report_tabular" ftype="tabular">
744 <assert_contents> 870 <assert_contents>
745 <has_text text="Vibrio_parahaemolyticus" /> 871 <has_text text="# contigs (>= 0 bp)"/>
872 <has_text text="contig1"/>
873 <has_text text="# N's per 100 kbp"/>
874 <has_n_lines n="22"/>
875 </assert_contents>
876 </output>
877 </test>
878 <!-- Test 12: Test paired-collection fastq.gz inputs -->
879 <test expect_num_outputs="1">
880 <conditional name="in">
881 <param name="custom" value="true"/>
882 <repeat name="inputs">
883 <param name="input" value="contigs1.fna"/>
884 <param name="labels" value="contig1"/>
885 </repeat>
886 </conditional>
887 <conditional name="reads">
888 <param name="reads_option" value="paired_collection"/>
889 <param name="input_1">
890 <collection type="paired">
891 <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
892 <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
893 </collection>
894 </param>
895 </conditional>
896 <conditional name="assembly">
897 <param name="type" value="genome"/>
898 <conditional name="ref">
899 <param name="use_ref" value="false"/>
900 </conditional>
901 </conditional>
902 <param name="output_files" value="tabular"/>
903 <output name="report_tabular" ftype="tabular">
904 <assert_contents>
905 <has_text text="# contigs (>= 0 bp)"/>
906 <has_text text="contig1"/>
907 <has_text text="# N's per 100 kbp"/>
908 <has_n_lines n="15"/>
746 </assert_contents> 909 </assert_contents>
747 </output> 910 </output>
748 </test> 911 </test>
749 </tests> 912 </tests>
750 <help> 913 <help>