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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69
author iuc
date Thu, 02 Mar 2023 10:38:54 +0000
parents 3061c8b029e5
children
comparison
equal deleted inserted replaced
14:3061c8b029e5 15:72472698a2df
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
9 <![CDATA[ 9 <![CDATA[
10 #import re 10 #import re
11 #import os 11 #import os
12 12
13 #if str($in.custom) == 'false' 13 #if str($mode.in.custom) == 'false'
14 #set $labels = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $in.inputs]) 14 #if $mode.mode == 'individual'
15 #set $labels = re.sub('[^\w\-_]', '_', str($mode.in.inputs.element_identifier))
16 #else
17 #set $labels = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $mode.in.inputs])
18 #end if
15 echo $labels && 19 echo $labels &&
16 #else 20 #else
17 #set $labels = [] 21 #if $mode.mode == 'individual'
18 #for $x in $in.inputs 22 #if str($mode.in.labels) != ''
19 #if str($x.labels) != '' 23 #set $labels = re.sub('[^\w\-_]', '_', str($mode.in.labels))
20 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.labels)))
21 #else 24 #else
22 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.input.element_identifier))) 25 #set $labels = re.sub('[^\w\-_]', '_', str($mode.in.input.element_identifier))
23 #end if 26 #end if
24 #end for 27 #else
25 #set $labels = ','.join($labels) 28 #set $labels = []
29 #for $x in $mode.in.inputs
30 #if str($x.labels) != ''
31 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.labels)))
32 #else
33 #silent $labels.append(re.sub('[^\w\-_]', '_', str($x.input.element_identifier)))
34 #end if
35 #end for
36 #set $labels = ','.join($labels)
37 #end if
26 #end if 38 #end if
27 39
28 #if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list' 40 #if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list'
29 #set $temp_ref_list_fp = 'temp_ref_list' 41 #set $temp_ref_list_fp = 'temp_ref_list'
30 #for $i in $assembly.ref.references_list.split(',') 42 #for $i in $assembly.ref.references_list.split(',')
31 echo $i >> $temp_ref_list_fp && 43 echo $i >> $temp_ref_list_fp &&
32 #end for 44 #end for
33 #end if 45 #end if
34 46
35 #if $reads.reads_option == 'paired' 47 #if $mode.reads.reads_option == 'paired'
36 #for $read in $reads.input_1 48 #if $mode.mode == 'individual'
37 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier)) 49 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
50 ln -s '$mode.reads.input_1' 'pe1-${identifier}.${mode.reads.input_1.ext}' &&
51 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_2.element_identifier))
52 ln -s '$mode.reads.input_2' 'pe2-${identifier}.${mode.reads.input_2.ext}' &&
53 #else
54 #for $read in $mode.reads.input_1
55 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
38 ln -s '$read' 'pe1-${identifier}.${read.ext}' && 56 ln -s '$read' 'pe1-${identifier}.${read.ext}' &&
39 #end for 57 #end for
40 #for $read in $reads.input_2 58 #for $read in $mode.reads.input_2
41 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier)) 59 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
42 ln -s '$read' 'pe2-${identifier}.${read.ext}' && 60 ln -s '$read' 'pe2-${identifier}.${read.ext}' &&
43 #end for 61 #end for
44 #else if $reads.reads_option == 'paired_collection' 62 #end if
45 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($reads.input_1.element_identifier)) 63 #else if $mode.reads.reads_option == 'paired_collection'
46 ln -s '$reads.input_1.forward' 'pe1-${identifier}.${reads.input_1.forward.ext}' && 64 #if $mode.mode == 'individual'
47 ln -s '$reads.input_1.reverse' 'pe2-${identifier}.${reads.input_1.reverse.ext}' && 65 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
66 ln -s '$mode.reads.input_1.forward' 'pe1-${identifier}.${mode.reads.input_1.forward.ext}' &&
67 ln -s '$mode.reads.input_1.reverse' 'pe2-${identifier}.${mode.reads.input_1.reverse.ext}' &&
68 #else
69 #for $read in $mode.reads.input_1
70 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
71 ln -s '$read.forward' 'pe1-${identifier}.${read.forward.ext}' &&
72 ln -s '$read.reverse' 'pe2-${identifier}.${read.reverse.ext}' &&
73 #end for
74 #end if
48 #end if 75 #end if
49 76
50 #if $assembly.type == 'genome' 77 #if $assembly.type == 'genome'
51 quast 78 quast
52 #else 79 #else
53 metaquast 80 metaquast
54 #end if 81 #end if
55 82
56 #if $reads.reads_option == 'single' 83 #if $mode.reads.reads_option == 'single'
57 #for $read in $reads.input_1 84 #if $mode.mode == 'individual'
85 --single '$mode.reads.input_1'
86 #else
87 #for $read in $mode.reads.input_1
58 --single '$read' 88 --single '$read'
59 #end for 89 #end for
60 #else if $reads.reads_option == 'paired' 90 #end if
61 #for $read in $reads.input_1 91 #else if $mode.reads.reads_option == 'paired'
62 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier)) 92 #if $mode.mode == 'individual'
93 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
94 --pe1 'pe1-${identifier}.${mode.reads.input_1.ext}'
95 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_2.element_identifier))
96 --pe2 'pe2-${identifier}.${mode.reads.input_2.ext}'
97 #else
98 #for $read in $mode.reads.input_1
99 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
63 --pe1 'pe1-${identifier}.${read.ext}' 100 --pe1 'pe1-${identifier}.${read.ext}'
64 #end for 101 #end for
65 #for $read in $reads.input_2 102 #for $read in $mode.reads.input_2
66 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier)) 103 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
67 --pe2 'pe2-${identifier}.${read.ext}' 104 --pe2 'pe2-${identifier}.${read.ext}'
68 #end for 105 #end for
69 #else if $reads.reads_option == 'paired_collection' 106 #end if
70 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($reads.input_1.element_identifier)) 107 #else if $mode.reads.reads_option == 'paired_collection'
71 --pe1 'pe1-${identifier}.${reads.input_1.forward.ext}' 108 #if $mode.mode == 'individual'
72 --pe2 'pe2-${identifier}.${reads.input_1.reverse.ext}' 109 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.reads.input_1.element_identifier))
73 #else if $reads.reads_option == 'paired_interlaced' 110 --pe1 'pe1-${identifier}.${mode.reads.input_1.forward.ext}'
74 #for $read in $reads.input_1 111 --pe2 'pe2-${identifier}.${mode.reads.input_1.reverse.ext}'
112 #else
113 #for $read in $mode.reads.input_1
114 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier))
115 --pe1 'pe1-${identifier}.${read.forward.ext}'
116 --pe2 'pe2-${identifier}.${read.reverse.ext}'
117 #end for
118 #end if
119 #else if $mode.reads.reads_option == 'paired_interlaced'
120 #if $mode.mode == 'individual'
121 --pe12 '$mode.reads.input_1'
122 #else
123 #for $read in $mode.reads.input_1
75 --pe12 '$read' 124 --pe12 '$read'
76 #end for 125 #end for
77 #else if $reads.reads_option == 'mate_paired' 126 #end if
78 #for $read in $reads.input_1 127 #else if $mode.reads.reads_option == 'mate_paired'
128 #if $mode.mode == 'individual'
129 --mp1 '$mode.reads.input_1'
130 --mp2 '$mode.reads.input_2'
131 #else
132 #for $read in $mode.reads.input_1
79 --mp1 '$read' 133 --mp1 '$read'
80 #end for 134 #end for
81 #for $read in $reads.input_2 135 #for $read in $mode.reads.input_2
82 --mp2 '$read' 136 --mp2 '$read'
83 #end for 137 #end for
84 #else if $reads.reads_option == 'pacbio' 138 #end if
85 #for $read in $reads.input_1 139 #else if $mode.reads.reads_option == 'pacbio'
140 #if $mode.mode == 'individual'
141 --pacbio '$mode.reads.input_1'
142 #else
143 #for $read in $mode.reads.input_1
86 --pacbio '$read' 144 --pacbio '$read'
87 #end for 145 #end for
88 #else if $reads.reads_option == 'nanopore' 146 #end if
89 #for $read in $reads.input_1 147 #else if $mode.reads.reads_option == 'nanopore'
148 #if $mode.mode == 'individual'
149 --nanopore '$mode.reads.input_1'
150 #else
151 #for $read in $mode.reads.input_1
90 --nanopore '$read' 152 --nanopore '$read'
91 #end for 153 #end for
154 #end if
92 #end if 155 #end if
93
94 --labels '$labels' 156 --labels '$labels'
95 -o 'outputdir' 157 -o 'outputdir'
96 158
97 #if $assembly.type == 'genome' 159 #if $assembly.type == 'genome'
98 #if $assembly.ref.use_ref == 'true' 160 #if $assembly.ref.use_ref == 'true'
116 #if $assembly.ref.origin == 'history' 178 #if $assembly.ref.origin == 'history'
117 -r '$assembly.ref.r' 179 -r '$assembly.ref.r'
118 #else if $assembly.ref.origin == 'list' 180 #else if $assembly.ref.origin == 'list'
119 --references-list '$temp_ref_list_fp' 181 --references-list '$temp_ref_list_fp'
120 #else if $assembly.ref.origin == 'silva' 182 #else if $assembly.ref.origin == 'silva'
121 --test-no-ref
122 --max-ref-num $assembly.ref.max_ref_num 183 --max-ref-num $assembly.ref.max_ref_num
123 #end if 184 #end if
124 $assembly.reuse_combined_alignments 185 $assembly.reuse_combined_alignments
125 #end if 186 #end if
126
127 --min-identity $assembly.min_identity 187 --min-identity $assembly.min_identity
128
129 --min-contig $min_contig 188 --min-contig $min_contig
130 $split_scaffolds 189 $split_scaffolds
131 $large 190 $large
132 191
133 #if str($genes.gene_finding.tool) != 'none' 192 #if str($genes.gene_finding.tool) != 'none'
167 --unaligned-part-size $advanced.unaligned_part_size 226 --unaligned-part-size $advanced.unaligned_part_size
168 $advanced.skip_unaligned_mis_contigs 227 $advanced.skip_unaligned_mis_contigs
169 $advanced.report_all_metrics 228 $advanced.report_all_metrics
170 --x-for-Nx $advanced.x_for_Nx 229 --x-for-Nx $advanced.x_for_Nx
171 230
172 #if str($in.custom) == 'false' 231 #if str($mode.in.custom) == 'false'
173 #for $k in $in.inputs 232 #if $mode.mode == 'individual'
233 '$mode.in.inputs'
234 #else
235 #for $k in $mode.in.inputs
174 '$k' 236 '$k'
175 #end for 237 #end for
238 #end if
176 #else 239 #else
177 #for $k in $in.inputs 240 #if $mode.mode == 'individual'
241 '$mode.in.input'
242 #else
243 #for $k in $mode.in.inputs
178 '$k.input' 244 '$k.input'
179 #end for 245 #end for
246 #end if
180 #end if 247 #end if
181 --threads \${GALAXY_SLOTS:-1} 248 --threads \${GALAXY_SLOTS:-1}
182 249
183 #if $assembly.type == 'genome' 250 #if $assembly.type == 'genome'
184 && mkdir -p '$report_html.files_path' 251 && mkdir -p '$report_html.files_path'
195 && if [[ -d "outputdir/combined_reference/icarus_viewers" ]]; then cp -R outputdir/combined_reference/icarus_viewers '$report_html_meta.files_path'; fi 262 && 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 '$krona.files_path'; fi 263 && if [[ -d "outputdir/krona_charts/" ]]; then mkdir -p '$krona.files_path' && cp outputdir/krona_charts/*.html '$krona.files_path'; fi
197 #end if 264 #end if
198 ]]></command> 265 ]]></command>
199 <inputs> 266 <inputs>
200 <conditional name="in"> 267 <conditional name="mode">
201 <param name="custom" type="select" label="Use customized names for the input files?" help="They will be used in reports, plots and logs"> 268 <param name="mode" type="select" label="Assembly mode?" help="Useful to know if contigs have been generated all samples together (co-assembly) or on each sample individually (individual assembly)">
202 <option value="true">Yes, specify custom names</option> 269 <option value="individual">Individual assembly (1 contig file per sample)</option>
203 <option value="false" selected="true">No, use dataset names</option> 270 <option value="co" selected="true">Co-assembly (1 contig file for several samples)</option>
204 </param> 271 </param>
205 <when value="true"> 272 <when value="individual">
206 <repeat name="inputs" title="Contigs/scaffolds" min="1"> 273 <conditional name="in">
207 <param name="input" type="data" format="fasta" label="Contigs/scaffolds file"/> 274 <expand macro="custom"/>
208 <param argument="--labels" type="text" value="" label="Name"/> 275 <when value="true">
209 </repeat> 276 <expand macro="labelled_input"/>
277 </when>
278 <when value="false">
279 <param name="inputs" type="data" format="fasta" label="Contigs/scaffolds file"/>
280 </when>
281 </conditional>
282 <conditional name="reads">
283 <expand macro="reads_option"/>
284 <when value="disabled"/>
285 <when value="single">
286 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file" />
287 </when>
288 <when value="paired">
289 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file #1" />
290 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file #2" />
291 </when>
292 <when value="paired_collection">
293 <param name="input_1" type="data_collection" collection_type="paired" format="fastq,fastq.gz,fasta,fasta.gz" label="FASTQ/FASTA files" />
294 </when>
295 <when value="paired_interlaced">
296 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file" />
297 </when>
298 <when value="mate_paired">
299 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file #1" />
300 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file #2" />
301 </when>
302 <when value="pacbio">
303 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file" />
304 </when>
305 <when value="nanopore">
306 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" label="FASTQ/FASTA file" />
307 </when>
308 </conditional>
210 </when> 309 </when>
211 <when value="false"> 310 <when value="co">
212 <param name="inputs" type="data" format="fasta" multiple="true" label="Contigs/scaffolds file"/> 311 <conditional name="in">
213 </when> 312 <expand macro="custom"/>
214 </conditional> 313 <when value="true">
215 <conditional name="reads"> 314 <repeat name="inputs" title="Contigs/scaffolds" min="1">
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."> 315 <expand macro="labelled_input"/>
217 <option value="disabled">Disabled</option> 316 </repeat>
218 <option value="single">Illumina single-end reads</option> 317 </when>
219 <option value="paired">Illumina paired-end reads</option> 318 <when value="false">
220 <option value="paired_collection">Illumina paired-end reads in paired collection</option> 319 <param name="inputs" type="data" format="fasta" multiple="true" label="Contigs/scaffolds file"/>
221 <option value="paired_interlaced">Illumina interlaced paired-end reads</option> 320 </when>
222 <option value="mate_paired">Illumina mate-pair reads</option> 321 </conditional>
223 <option value="pacbio">Pacbio SMRT reads</option> 322 <conditional name="reads">
224 <option value="nanopore">Nanopore reads</option> 323 <expand macro="reads_option"/>
225 </param> 324 <when value="disabled"/>
226 <when value="disabled"/> 325 <when value="single">
227 <when value="single"> 326 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
228 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" /> 327 </when>
229 </when> 328 <when value="paired">
230 <when value="paired"> 329 <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" /> 330 <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" /> 331 </when>
233 </when> 332 <when value="paired_collection">
234 <when value="paired_collection"> 333 <param name="input_1" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz,fasta,fasta.gz" label="FASTQ/FASTA files" />
235 <param name="input_1" type="data_collection" collection_type="paired" format="fastq,fastq.gz,fasta,fasta.gz" label="FASTQ/FASTA files" /> 334 </when>
236 </when> 335 <when value="paired_interlaced">
237 <when value="paired_interlaced"> 336 <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" /> 337 </when>
239 </when> 338 <when value="mate_paired">
240 <when value="mate_paired"> 339 <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" /> 340 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
242 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" /> 341 </when>
243 </when> 342 <when value="pacbio">
244 <when value="pacbio"> 343 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
245 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" /> 344 </when>
246 </when> 345 <when value="nanopore">
247 <when value="nanopore"> 346 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
248 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" /> 347 </when>
348 </conditional>
249 </when> 349 </when>
250 </conditional> 350 </conditional>
251 <conditional name="assembly"> 351 <conditional name="assembly">
252 <param name="type" type="select" label="Type of assembly"> 352 <param name="type" type="select" label="Type of assembly">
253 <option value="genome">Genome</option> 353 <option value="genome">Genome</option>
267 <param argument="--k-mer-stats" type="select" label="Compute k-mer-based quality metrics?" help="It is recommended for large genomes. This may significantly increase memory and time consumption on large genomes"> 367 <param argument="--k-mer-stats" type="select" label="Compute k-mer-based quality metrics?" help="It is recommended for large genomes. This may significantly increase memory and time consumption on large genomes">
268 <option value="--k-mer-stats">Yes</option> 368 <option value="--k-mer-stats">Yes</option>
269 <option value="" selected="true">No</option> 369 <option value="" selected="true">No</option>
270 </param> 370 </param>
271 <when value="--k-mer-stats"> 371 <when value="--k-mer-stats">
272 <param name="k_mer_size" argument="--k-mer-size" type="integer" value="101" label="Size of k" /> 372 <param argument="--k-mer-size" type="integer" value="101" label="Size of k" />
273 </when> 373 </when>
274 <when value=""/> 374 <when value=""/>
275 </conditional> 375 </conditional>
276 <param argument="--circos" type="boolean" truevalue="--circos" falsevalue="" checked="false" label="Generage Circos plot" help="Plot Circos version of Icarus contig alignment viewer"/> 376 <param argument="--circos" type="boolean" truevalue="--circos" falsevalue="" checked="false" label="Generage Circos plot" help="Plot Circos version of Icarus contig alignment viewer"/>
277 </when> 377 </when>
286 </param> 386 </param>
287 <expand macro="min_identity_macros" value="95"/> 387 <expand macro="min_identity_macros" value="95"/>
288 </when> 388 </when>
289 <when value="metagenome"> 389 <when value="metagenome">
290 <conditional name="ref"> 390 <conditional name="ref">
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."> 391 <param name="origin" type="select" label="Reference genome" help="If no reference genomes is provided, the tool will try to identify genome content of the metagenome. By default, it will align contigs to SILVA 16S rRNA database, i.e. FASTA file containing small subunit ribosomal RNA sequences to identify genomes. The reference genomes for the chosen genomes are downloaded from the NCBI database. After that, Quast is run on all of them. Reference genomes with low genome fraction (less than 10%) are removed. The usual MetaQUAST analysis continues with the remaining references.">
392 <option value="silva" selected="true">From SILVA database</option>
292 <option value="history">From history</option> 393 <option value="history">From history</option>
293 <option value="list">From list</option> 394 <option value="list">From a list</option>
294 <option value="silva">From SILVA database</option>
295 <option value="none" selected="true">None</option>
296 </param> 395 </param>
396 <when value="silva">
397 <param 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" />
398 </when>
297 <when value="history"> 399 <when value="history">
298 <param argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" /> 400 <param argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" />
299 </when> 401 </when>
300 <when value="list"> 402 <when value="list">
301 <param name="references_list" argument="references-list" type="text" value="" label="Comma-separated list of reference genomes" help="MetaQUAST will search for these references in the NCBI database and will download the found ones"/> 403 <param argument="--references-list" type="text" value="" label="Comma-separated list of reference genomes" help="MetaQUAST will search for these references in the NCBI database and will download the found ones"/>
302 </when> 404 </when>
303 <when value="silva">
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" />
305 </when>
306 <when value="none"/>
307 </conditional> 405 </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" /> 406 <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"/> 407 <expand macro="min_identity_macros" value="90"/>
310 </when> 408 </when>
311 </conditional> 409 </conditional>
383 <filter>assembly['type'] == 'genome' and 'pdf' in output_files</filter> 481 <filter>assembly['type'] == 'genome' and 'pdf' in output_files</filter>
384 </data> 482 </data>
385 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/quast.log"> 483 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/quast.log">
386 <filter>assembly['type'] == 'genome' and 'log' in output_files</filter> 484 <filter>assembly['type'] == 'genome' and 'log' in output_files</filter>
387 </data> 485 </data>
388 <data name="log_meta" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/metaquast.log"> 486 <data name="log_meta" format="txt" label="${tool.name} on ${on_string}: Log Meta" from_work_dir="outputdir/metaquast.log">
389 <filter>assembly['type'] == 'metagenome' and 'log' in output_files</filter> 487 <filter>assembly['type'] == 'metagenome' and 'log' in output_files</filter>
390 </data> 488 </data>
391 <data name="mis_ass" format="tabular" label="${tool.name} on ${on_string}: Misassemblies report" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt"> 489 <data name="mis_ass" format="tabular" label="${tool.name} on ${on_string}: Misassemblies report" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt">
392 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter> 490 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter>
393 <filter>'tabular' in output_files</filter> 491 <filter>'tabular' in output_files</filter>
416 </data> 514 </data>
417 </outputs> 515 </outputs>
418 <tests> 516 <tests>
419 <!-- Test 01: reference, genes annotations and operon coordinates --> 517 <!-- Test 01: reference, genes annotations and operon coordinates -->
420 <test expect_num_outputs="2"> 518 <test expect_num_outputs="2">
421 <conditional name="in"> 519 <conditional name="mode">
422 <param name="custom" value="true"/> 520 <param name="mode" value="co"/>
423 <repeat name="inputs"> 521 <conditional name="in">
424 <param name="input" value="contigs1.fna"/> 522 <param name="custom" value="true"/>
425 <param name="labels" value="contig1"/> 523 <repeat name="inputs">
426 </repeat> 524 <param name="input" value="contigs1.fna"/>
427 <repeat name="inputs"> 525 <param name="labels" value="contig1"/>
428 <param name="input" value="contigs2.fna"/> 526 </repeat>
429 <param name="labels" value="contig2"/> 527 <repeat name="inputs">
430 </repeat> 528 <param name="input" value="contigs2.fna"/>
529 <param name="labels" value="contig2"/>
530 </repeat>
531 </conditional>
431 </conditional> 532 </conditional>
432 <conditional name="assembly"> 533 <conditional name="assembly">
433 <param name="type" value="genome"/> 534 <param name="type" value="genome"/>
434 <conditional name="ref"> 535 <conditional name="ref">
435 <param name="use_ref" value="true"/> 536 <param name="use_ref" value="true"/>
474 <output name="report_html" file="test1_report.html" ftype="html" compare="sim_size"/> 575 <output name="report_html" file="test1_report.html" ftype="html" compare="sim_size"/>
475 <output name="circos_output" file="test1_circos.png" ftype="png" compare="sim_size"/> 576 <output name="circos_output" file="test1_circos.png" ftype="png" compare="sim_size"/>
476 </test> 577 </test>
477 <!-- Test 02: all outputs --> 578 <!-- Test 02: all outputs -->
478 <test expect_num_outputs="8"> 579 <test expect_num_outputs="8">
479 <conditional name="in"> 580 <conditional name="mode">
480 <param name="custom" value="true"/> 581 <param name="mode" value="co"/>
481 <repeat name="inputs"> 582 <conditional name="in">
482 <param name="input" value="contigs1.fna"/> 583 <param name="custom" value="true"/>
483 <param name="labels" value="contig1"/> 584 <repeat name="inputs">
484 </repeat> 585 <param name="input" value="contigs1.fna"/>
485 <repeat name="inputs"> 586 <param name="labels" value="contig1"/>
486 <param name="input" value="contigs2.fna"/> 587 </repeat>
487 <param name="labels" value="contig2"/> 588 <repeat name="inputs">
488 </repeat> 589 <param name="input" value="contigs2.fna"/>
590 <param name="labels" value="contig2"/>
591 </repeat>
592 </conditional>
489 </conditional> 593 </conditional>
490 <conditional name="assembly"> 594 <conditional name="assembly">
491 <param name="type" value="genome"/> 595 <param name="type" value="genome"/>
492 <conditional name="ref"> 596 <conditional name="ref">
493 <param name="use_ref" value="true"/> 597 <param name="use_ref" value="true"/>
511 <output name="kmers" file="test2_kmers.tab" ftype="tabular"/> 615 <output name="kmers" file="test2_kmers.tab" ftype="tabular"/>
512 <output name="circos_output" file="test2_circos.png" ftype="png" compare="sim_size"/> 616 <output name="circos_output" file="test2_circos.png" ftype="png" compare="sim_size"/>
513 </test> 617 </test>
514 <!-- Test 03: without reference --> 618 <!-- Test 03: without reference -->
515 <test expect_num_outputs="3"> 619 <test expect_num_outputs="3">
516 <conditional name="in"> 620 <conditional name="mode">
517 <param name="custom" value="false"/> 621 <param name="mode" value="individual"/>
518 <param name="inputs" value="contigs1.fna,contigs2.fna"/> 622 <conditional name="in">
623 <param name="custom" value="false"/>
624 <param name="inputs" value="contigs1.fna"/>
625 </conditional>
519 </conditional> 626 </conditional>
520 <conditional name="assembly"> 627 <conditional name="assembly">
521 <param name="type" value="genome"/> 628 <param name="type" value="genome"/>
522 <conditional name="ref"> 629 <conditional name="ref">
523 <param name="use_ref" value="false"/> 630 <param name="use_ref" value="false"/>
555 <output name="report_html" file="test3_report.html" compare="sim_size"/> 662 <output name="report_html" file="test3_report.html" compare="sim_size"/>
556 <output name="report_pdf" file="test3_report.pdf" compare="sim_size"/> 663 <output name="report_pdf" file="test3_report.pdf" compare="sim_size"/>
557 </test> 664 </test>
558 <!-- Test 04: metagenomics --> 665 <!-- Test 04: metagenomics -->
559 <test expect_num_outputs="3"> 666 <test expect_num_outputs="3">
560 <conditional name="in"> 667 <conditional name="mode">
561 <param name="custom" value="false"/> 668 <param name="mode" value="individual"/>
562 <param name="inputs" value="contigs3.fasta"/> 669 <conditional name="in">
670 <param name="custom" value="false"/>
671 <param name="inputs" value="contigs3.fasta"/>
672 </conditional>
563 </conditional> 673 </conditional>
564 <conditional name="assembly"> 674 <conditional name="assembly">
565 <param name="type" value="metagenome"/> 675 <param name="type" value="metagenome"/>
566 <conditional name="ref"> 676 <conditional name="ref">
567 <param name="origin" value="none"/> 677 <param name="origin" value="silva"/>
678 <param name="max_ref_num" value="50"/>
568 </conditional> 679 </conditional>
569 </conditional> 680 </conditional>
570 <param name="min_contig" value="500"/> 681 <param name="min_contig" value="500"/>
571 <param name="split_scaffolds" value="false"/> 682 <param name="split_scaffolds" value="false"/>
572 <param name="large" value="false"/> 683 <param name="large" value="false"/>
615 </assert_contents> 726 </assert_contents>
616 </output> 727 </output>
617 </test> 728 </test>
618 <!-- Test 05: FASTQ read files --> 729 <!-- Test 05: FASTQ read files -->
619 <test expect_num_outputs="3"> 730 <test expect_num_outputs="3">
620 <conditional name="in"> 731 <conditional name="mode">
621 <param name="custom" value="true"/> 732 <param name="mode" value="co"/>
622 <repeat name="inputs"> 733 <conditional name="in">
623 <param name="input" value="contigs1.fna"/> 734 <param name="custom" value="true"/>
624 <param name="labels" value="contig1"/> 735 <repeat name="inputs">
625 </repeat> 736 <param name="input" value="contigs1.fna"/>
626 <repeat name="inputs"> 737 <param name="labels" value="contig1"/>
627 <param name="input" value="contigs2.fna"/> 738 </repeat>
628 <param name="labels" value="contig2"/> 739 <repeat name="inputs">
629 </repeat> 740 <param name="input" value="contigs2.fna"/>
630 </conditional> 741 <param name="labels" value="contig2"/>
631 <conditional name="reads"> 742 </repeat>
632 <param name="reads_option" value="pacbio"/> 743 </conditional>
633 <param name="input_1" value="pacbio_01.fastq,pacbio_02.fastq,pacbio_03.fastq,pacbio_04.fastq"/> 744 <conditional name="reads">
745 <param name="reads_option" value="pacbio"/>
746 <param name="input_1" value="pacbio_01.fastq,pacbio_02.fastq,pacbio_03.fastq,pacbio_04.fastq"/>
747 </conditional>
634 </conditional> 748 </conditional>
635 <conditional name="assembly"> 749 <conditional name="assembly">
636 <param name="type" value="genome"/> 750 <param name="type" value="genome"/>
637 <conditional name="ref"> 751 <conditional name="ref">
638 <param name="use_ref" value="true"/> 752 <param name="use_ref" value="true"/>
659 </assert_contents> 773 </assert_contents>
660 </output> 774 </output>
661 </test> 775 </test>
662 <!-- Test 06: FASTQ.gz read files --> 776 <!-- Test 06: FASTQ.gz read files -->
663 <test expect_num_outputs="1"> 777 <test expect_num_outputs="1">
664 <conditional name="in"> 778 <conditional name="mode">
665 <param name="custom" value="true"/> 779 <param name="mode" value="co"/>
666 <repeat name="inputs"> 780 <conditional name="in">
667 <param name="input" value="contigs1.fna"/> 781 <param name="custom" value="true"/>
668 <param name="labels" value="contig1"/> 782 <repeat name="inputs">
669 </repeat> 783 <param name="input" value="contigs1.fna"/>
670 <repeat name="inputs"> 784 <param name="labels" value="contig1"/>
671 <param name="input" value="contigs2.fna"/> 785 </repeat>
672 <param name="labels" value="contig2"/> 786 <repeat name="inputs">
673 </repeat> 787 <param name="input" value="contigs2.fna"/>
674 </conditional> 788 <param name="labels" value="contig2"/>
675 <conditional name="reads"> 789 </repeat>
676 <param name="reads_option" value="single"/> 790 </conditional>
677 <param name="input_1" value="pacbio_01.fastq.gz,pacbio_02.fastq.gz"/> 791 <conditional name="reads">
792 <param name="reads_option" value="single"/>
793 <param name="input_1" value="pacbio_01.fastq.gz,pacbio_02.fastq.gz"/>
794 </conditional>
678 </conditional> 795 </conditional>
679 <param name="output_files" value="tabular"/> 796 <param name="output_files" value="tabular"/>
680 <output name="report_tabular" file="test6.tab" ftype="tabular"/> 797 <output name="report_tabular" file="test6.tab" ftype="tabular"/>
681 </test> 798 </test>
682 <!-- Test 07: FASTA.gz read files --> 799 <!-- Test 07: FASTA.gz read files -->
683 <test expect_num_outputs="1"> 800 <test expect_num_outputs="1">
684 <conditional name="in"> 801 <conditional name="mode">
685 <param name="custom" value="true"/> 802 <param name="mode" value="co"/>
686 <repeat name="inputs"> 803 <conditional name="in">
687 <param name="input" value="contigs1.fna"/> 804 <param name="custom" value="true"/>
688 <param name="labels" value="contig1"/> 805 <repeat name="inputs">
689 </repeat> 806 <param name="input" value="contigs1.fna"/>
690 <repeat name="inputs"> 807 <param name="labels" value="contig1"/>
691 <param name="input" value="contigs2.fna"/> 808 </repeat>
692 <param name="labels" value="contig2"/> 809 <repeat name="inputs">
693 </repeat> 810 <param name="input" value="contigs2.fna"/>
694 </conditional> 811 <param name="labels" value="contig2"/>
695 <conditional name="reads"> 812 </repeat>
696 <param name="reads_option" value="single"/> 813 </conditional>
697 <param name="input_1" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> 814 <conditional name="reads">
815 <param name="reads_option" value="single"/>
816 <param name="input_1" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
817 </conditional>
698 </conditional> 818 </conditional>
699 <param name="output_files" value="tabular"/> 819 <param name="output_files" value="tabular"/>
700 <output name="report_tabular" file="test7.tab" ftype="tabular"/> 820 <output name="report_tabular" file="test7.tab" ftype="tabular"/>
701 </test> 821 </test>
702 <!-- Test 08: metagenomics all tab outputs--> 822 <!-- Test 08: metagenomics all tab outputs-->
703 <test expect_num_outputs="3"> 823 <test expect_num_outputs="3">
704 <conditional name="in"> 824 <conditional name="mode">
705 <repeat name="inputs"> 825 <param name="mode" value="co"/>
706 <param name="input" value="meta_contigs_1.fasta"/> 826 <conditional name="in">
707 <param name="labels" value="meta_contigs_1"/> 827 <repeat name="inputs">
708 </repeat> 828 <param name="input" value="meta_contigs_1.fasta"/>
709 <repeat name="inputs"> 829 <param name="labels" value="meta_contigs_1"/>
710 <param name="input" value="meta_contigs_2.fasta"/> 830 </repeat>
711 <param name="labels" value="meta_contigs_2"/> 831 <repeat name="inputs">
712 </repeat> 832 <param name="input" value="meta_contigs_2.fasta"/>
833 <param name="labels" value="meta_contigs_2"/>
834 </repeat>
835 </conditional>
713 </conditional> 836 </conditional>
714 <conditional name="assembly"> 837 <conditional name="assembly">
715 <param name="type" value="metagenome"/> 838 <param name="type" value="metagenome"/>
716 <conditional name="ref"> 839 <conditional name="ref">
717 <param name="origin" value="history"/> 840 <param name="origin" value="history"/>
756 <output_collection name="metrics_tabular" type="list" count="15"/> 879 <output_collection name="metrics_tabular" type="list" count="15"/>
757 <output_collection name="metrics_pdf" type="list" count="16"/> 880 <output_collection name="metrics_pdf" type="list" count="16"/>
758 </test> 881 </test>
759 <!-- Test 09: metagenomics log, html and krona outputs--> 882 <!-- Test 09: metagenomics log, html and krona outputs-->
760 <test expect_num_outputs="2"> 883 <test expect_num_outputs="2">
761 <conditional name="in"> 884 <conditional name="mode">
762 <repeat name="inputs"> 885 <param name="mode" value="co"/>
763 <param name="input" value="meta_contigs_1.fasta"/> 886 <conditional name="in">
764 <param name="labels" value="meta_contigs_1"/> 887 <repeat name="inputs">
765 </repeat> 888 <param name="input" value="meta_contigs_1.fasta"/>
766 <repeat name="inputs"> 889 <param name="labels" value="meta_contigs_1"/>
767 <param name="input" value="meta_contigs_2.fasta"/> 890 </repeat>
768 <param name="labels" value="meta_contigs_2"/> 891 <repeat name="inputs">
769 </repeat> 892 <param name="input" value="meta_contigs_2.fasta"/>
893 <param name="labels" value="meta_contigs_2"/>
894 </repeat>
895 </conditional>
770 </conditional> 896 </conditional>
771 <conditional name="assembly"> 897 <conditional name="assembly">
772 <param name="type" value="metagenome"/> 898 <param name="type" value="metagenome"/>
773 <conditional name="ref"> 899 <conditional name="ref">
774 <param name="origin" value="list"/> 900 <param name="origin" value="list"/>
816 </assert_contents> 942 </assert_contents>
817 </output> 943 </output>
818 </test> 944 </test>
819 <!-- Test 10: Test new options --> 945 <!-- Test 10: Test new options -->
820 <test expect_num_outputs="1"> 946 <test expect_num_outputs="1">
821 <conditional name="in"> 947 <conditional name="mode">
822 <param name="custom" value="true"/> 948 <param name="mode" value="co"/>
823 <repeat name="inputs"> 949 <conditional name="in">
824 <param name="input" value="contigs1.fna"/> 950 <param name="custom" value="true"/>
825 <param name="labels" value="contig1"/> 951 <repeat name="inputs">
826 </repeat> 952 <param name="input" value="contigs1.fna"/>
827 <repeat name="inputs"> 953 <param name="labels" value="contig1"/>
828 <param name="input" value="contigs2.fna"/> 954 </repeat>
829 <param name="labels" value="contig2"/> 955 <repeat name="inputs">
830 </repeat> 956 <param name="input" value="contigs2.fna"/>
957 <param name="labels" value="contig2"/>
958 </repeat>
959 </conditional>
831 </conditional> 960 </conditional>
832 <section name="alignments"> 961 <section name="alignments">
833 <param name="local_mis_size" value="210"/> 962 <param name="local_mis_size" value="210"/>
834 </section> 963 </section>
835 <conditional name="assembly"> 964 <conditional name="assembly">
845 <param name="output_files" value="tabular"/> 974 <param name="output_files" value="tabular"/>
846 <output name="report_tabular" file="test10_tabular_report.tab" ftype="tabular"/> 975 <output name="report_tabular" file="test10_tabular_report.tab" ftype="tabular"/>
847 </test> 976 </test>
848 <!-- Test 11: Test paired fastq.gz inputs --> 977 <!-- Test 11: Test paired fastq.gz inputs -->
849 <test expect_num_outputs="1"> 978 <test expect_num_outputs="1">
850 <conditional name="in"> 979 <conditional name="mode">
851 <param name="custom" value="true"/> 980 <param name="mode" value="individual"/>
852 <repeat name="inputs"> 981 <conditional name="in">
982 <param name="custom" value="true"/>
853 <param name="input" value="contigs1.fna"/> 983 <param name="input" value="contigs1.fna"/>
854 <param name="labels" value="contig1"/> 984 <param name="labels" value="contig1"/>
855 </repeat> 985 </conditional>
856 </conditional> 986 <conditional name="reads">
857 <conditional name="reads"> 987 <param name="reads_option" value="paired"/>
858 <param name="reads_option" value="paired"/> 988 <param name="input_1" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
859 <param name="input_1" value="reads1.fastq.gz" ftype="fastqsanger.gz"/> 989 <param name="input_2" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
860 <param name="input_2" value="reads2.fastq.gz" ftype="fastqsanger.gz"/> 990 </conditional>
861 </conditional> 991 </conditional>
862 <conditional name="assembly"> 992 <conditional name="assembly">
863 <param name="type" value="genome"/> 993 <param name="type" value="genome"/>
864 <conditional name="ref"> 994 <conditional name="ref">
865 <param name="use_ref" value="false"/> 995 <param name="use_ref" value="false"/>
875 </assert_contents> 1005 </assert_contents>
876 </output> 1006 </output>
877 </test> 1007 </test>
878 <!-- Test 12: Test paired-collection fastq.gz inputs --> 1008 <!-- Test 12: Test paired-collection fastq.gz inputs -->
879 <test expect_num_outputs="1"> 1009 <test expect_num_outputs="1">
880 <conditional name="in"> 1010 <conditional name="mode">
881 <param name="custom" value="true"/> 1011 <param name="mode" value="individual"/>
882 <repeat name="inputs"> 1012 <conditional name="in">
1013 <param name="custom" value="true"/>
883 <param name="input" value="contigs1.fna"/> 1014 <param name="input" value="contigs1.fna"/>
884 <param name="labels" value="contig1"/> 1015 <param name="labels" value="contig1"/>
885 </repeat> 1016 </conditional>
886 </conditional> 1017 <conditional name="reads">
887 <conditional name="reads"> 1018 <param name="reads_option" value="paired_collection"/>
888 <param name="reads_option" value="paired_collection"/> 1019 <param name="input_1">
889 <param name="input_1"> 1020 <collection type="paired">
890 <collection type="paired"> 1021 <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
891 <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/> 1022 <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
892 <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/> 1023 </collection>
893 </collection> 1024 </param>
894 </param> 1025 </conditional>
895 </conditional> 1026 </conditional>
896 <conditional name="assembly"> 1027 <conditional name="assembly">
897 <param name="type" value="genome"/> 1028 <param name="type" value="genome"/>
898 <conditional name="ref"> 1029 <conditional name="ref">
899 <param name="use_ref" value="false"/> 1030 <param name="use_ref" value="false"/>
904 <assert_contents> 1035 <assert_contents>
905 <has_text text="# contigs (>= 0 bp)"/> 1036 <has_text text="# contigs (>= 0 bp)"/>
906 <has_text text="contig1"/> 1037 <has_text text="contig1"/>
907 <has_text text="# N's per 100 kbp"/> 1038 <has_text text="# N's per 100 kbp"/>
908 <has_n_lines n="15"/> 1039 <has_n_lines n="15"/>
1040 </assert_contents>
1041 </output>
1042 </test>
1043 <!-- Test 13: Test co-assembly with paired-collection fastq.gz inputs -->
1044 <test expect_num_outputs="1">
1045 <conditional name="mode">
1046 <param name="mode" value="co"/>
1047 <conditional name="in">
1048 <param name="custom" value="false"/>
1049 <param name="inputs" value="contigs1.fna,contigs2.fna"/>
1050 </conditional>
1051 <conditional name="reads">
1052 <param name="reads_option" value="paired_collection"/>
1053 <param name="input_1">
1054 <collection type="list:paired">
1055 <element name="s1">
1056 <collection type="paired">
1057 <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
1058 <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
1059 </collection>
1060 </element>
1061 <element name="s2">
1062 <collection type="paired">
1063 <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>
1064 <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>
1065 </collection>
1066 </element>
1067 </collection>
1068 </param>
1069 </conditional>
1070 </conditional>
1071 <conditional name="assembly">
1072 <param name="type" value="genome"/>
1073 <conditional name="ref">
1074 <param name="use_ref" value="false"/>
1075 </conditional>
1076 </conditional>
1077 <param name="output_files" value="tabular"/>
1078 <output name="report_tabular" ftype="tabular">
1079 <assert_contents>
1080 <has_text text="# contigs (>= 0 bp)"/>
1081 <has_text text="contigs1"/>
1082 <has_text text="# N's per 100 kbp"/>
1083 <has_n_lines n="22"/>
909 </assert_contents> 1084 </assert_contents>
910 </output> 1085 </output>
911 </test> 1086 </test>
912 </tests> 1087 </tests>
913 <help> 1088 <help>