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comparison quast.xml @ 14:459ceb2ff536 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
author iuc
date Fri, 25 Mar 2022 17:36:16 +0000
parents 74be236ac5fd
children 25368452f73b
comparison
equal deleted inserted replaced
13:74be236ac5fd 14:459ceb2ff536
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
7 <expand macro='requirements' /> 7 <expand macro='requirements' />
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 12
12 #if str($in.custom) == 'false' 13 #if str($in.custom) == 'false'
13 #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])
14 echo $labels && 15 echo $labels &&
15 #else 16 #else
45 #for $read in $reads.input_1 46 #for $read in $reads.input_1
46 --pe1 '$read' 47 --pe1 '$read'
47 #end for 48 #end for
48 #for $read in $reads.input_2 49 #for $read in $reads.input_2
49 --pe2 '$read' 50 --pe2 '$read'
50 #end for 51 #end for
51 #else if $reads.reads_option == 'paired_interlaced' 52 #else if $reads.reads_option == 'paired_interlaced'
52 #for $read in $reads.input_1 53 #for $read in $reads.input_1
53 --pe12 '$read' 54 --pe12 '$read'
54 #end for 55 #end for
55 #else if $reads.reads_option == 'mate_paired' 56 #else if $reads.reads_option == 'mate_paired'
67 #for $read in $reads.input_1 68 #for $read in $reads.input_1
68 --nanopore '$read' 69 --nanopore '$read'
69 #end for 70 #end for
70 #end if 71 #end if
71 72
72 --labels $labels 73 --labels '$labels'
73 -o outputdir 74 -o 'outputdir'
74 75
75 #if $assembly.type == 'genome' 76 #if $assembly.type == 'genome'
76 #if $assembly.ref.use_ref == 'true' 77 #if $assembly.ref.use_ref == 'true'
77 -r '$assembly.ref.r' 78 -r '$assembly.ref.r'
78 #if $assembly.ref.features 79 #if $assembly.ref.features
95 -r '$assembly.ref.r' 96 -r '$assembly.ref.r'
96 #else if $assembly.ref.origin == 'list' 97 #else if $assembly.ref.origin == 'list'
97 --references-list '$temp_ref_list_fp' 98 --references-list '$temp_ref_list_fp'
98 #else if $assembly.ref.origin == 'silva' 99 #else if $assembly.ref.origin == 'silva'
99 --test-no-ref 100 --test-no-ref
100 --max-ref-num '$assembly.ref.max_ref_num' 101 --max-ref-num $assembly.ref.max_ref_num
101 #end if 102 #end if
102 #end if 103 #end if
103 104
104 --min-contig $min_contig 105 --min-contig $min_contig
105 $split_scaffolds 106 $split_scaffolds
117 $genes.conserved_genes_finding 118 $genes.conserved_genes_finding
118 $alignments.use_all_alignments 119 $alignments.use_all_alignments
119 --min-alignment $alignments.min_alignment 120 --min-alignment $alignments.min_alignment
120 --min-identity $alignments.min_identity 121 --min-identity $alignments.min_identity
121 --ambiguity-usage '$alignments.ambiguity_usage' 122 --ambiguity-usage '$alignments.ambiguity_usage'
122 --ambiguity-score '$alignments.ambiguity_score' 123 --ambiguity-score $alignments.ambiguity_score
123 $alignments.fragmented 124 $alignments.fragmented
124 $alignments.upper_bound_assembly 125 $alignments.upper_bound_assembly
125 #if $alignments.upper_bound_min_con 126 #if $alignments.upper_bound_min_con
126 --upper-bound-min-con $alignments.upper_bound_min_con 127 --upper-bound-min-con $alignments.upper_bound_min_con
127 #end if 128 #end if
155 && mkdir -p '$report_html.files_path' 156 && mkdir -p '$report_html.files_path'
156 && cp outputdir/*.html '$report_html.files_path' 157 && cp outputdir/*.html '$report_html.files_path'
157 158
158 #if ($assembly.type == 'genome' and $assembly.ref.use_ref) or ($assembly.type == 'metagenome' and $assembly.ref.origin != 'none') 159 #if ($assembly.type == 'genome' and $assembly.ref.use_ref) or ($assembly.type == 'metagenome' and $assembly.ref.origin != 'none')
159 && cp -R outputdir/icarus_viewers '$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
160 #end if 169 #end if
161 170
162 ]]> 171 ]]>
163 </command> 172 </command>
164 <inputs> 173 <inputs>
186 <option value="mate_paired">Illumina mate-pair reads</option> 195 <option value="mate_paired">Illumina mate-pair reads</option>
187 <option value="pacbio">Pacbio SMRT reads</option> 196 <option value="pacbio">Pacbio SMRT reads</option>
188 <option value="nanopore">Nanopore reads</option> 197 <option value="nanopore">Nanopore reads</option>
189 </param> 198 </param>
190 <when value="disabled"/> 199 <when value="disabled"/>
191
192 <when value="single"> 200 <when value="single">
193 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" /> 201 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
194 </when> 202 </when>
195
196 <when value="paired"> 203 <when value="paired">
197 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" /> 204 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
198 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" /> 205 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
199 </when> 206 </when>
200 207
201 <when value="paired_interlaced"> 208 <when value="paired_interlaced">
202 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" /> 209 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
203 </when> 210 </when>
204
205 <when value="mate_paired"> 211 <when value="mate_paired">
206 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" /> 212 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
207 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" /> 213 <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
208 </when> 214 </when>
209
210 <when value="pacbio"> 215 <when value="pacbio">
211 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" /> 216 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
212 </when> 217 </when>
213
214 <when value="nanopore"> 218 <when value="nanopore">
215 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" /> 219 <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
216 </when> 220 </when>
217 </conditional> 221 </conditional>
218
219 <conditional name="assembly"> 222 <conditional name="assembly">
220 <param name="type" type="select" label="Type of assembly"> 223 <param name="type" type="select" label="Type of assembly">
221 <option value="genome">Genome</option> 224 <option value="genome">Genome</option>
222 <option value="metagenome">Metagenome</option> 225 <option value="metagenome">Metagenome</option>
223 </param> 226 </param>
319 <param argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/> 322 <param argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/>
320 <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)."/> 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)."/>
321 <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" /> 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" />
322 </section> 325 </section>
323 <param name="output_files" type="select" display="checkboxes" optional="true" multiple="true" label="Output files"> 326 <param name="output_files" type="select" display="checkboxes" optional="true" multiple="true" label="Output files">
324 <option value="html" selected="true">HTML report</option> 327 <option value="html" selected="true">HTML reports</option>
325 <option value="pdf">PDF report</option> 328 <option value="pdf">PDF reports</option>
326 <option value="tabular">Tabular reports</option> 329 <option value="tabular">Tabular reports</option>
327 <option value="log">Log file</option> 330 <option value="log">Log file</option>
331 <option value="summary">Key metric summary (metagenome mode)</option>
332 <option value="krona">Krona charts (metagenome mode without reference genomes)</option>
328 </param> 333 </param>
329 </inputs> 334 </inputs>
330 <outputs> 335 <outputs>
331 <data name="quast_tabular" format="tabular" label="${tool.name} on ${on_string}: tabular report" from_work_dir="outputdir/report.tsv"> 336 <data name="report_tabular" format="tabular" label="${tool.name} on ${on_string}: tabular report" from_work_dir="outputdir/report.tsv">
332 <filter>'tabular' in output_files</filter> 337 <filter>assembly['type'] == 'genome' and 'tabular' in output_files</filter>
333 </data> 338 </data>
334 <data name="report_html" format="html" label="${tool.name} on ${on_string}: HTML report" from_work_dir="outputdir/report.html"> 339 <data name="report_tabular_meta" format="tabular" label="${tool.name} on ${on_string}: tabular report for combined reference genome" from_work_dir="outputdir/combined_reference/report.tsv">
340 <filter>assembly['type'] == 'metagenome' and 'tabular' in output_files</filter>
341 </data>
342 <data name="report_html" format="html" label="${tool.name} on ${on_string}: HTML report" from_work_dir="outputdir/report.html">
335 <filter>'html' in output_files</filter> 343 <filter>'html' in output_files</filter>
336 </data> 344 </data>
345 <data name="report_html_meta" format="html" label="${tool.name} on ${on_string}: HTML report for combined reference genome" from_work_dir="outputdir/combined_reference/report.html">
346 <filter>assembly['type'] == 'metagenome' and 'html' in output_files</filter>
347 </data>
337 <data name="report_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF report" from_work_dir="outputdir/report.pdf"> 348 <data name="report_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF report" from_work_dir="outputdir/report.pdf">
338 <filter>'pdf' in output_files</filter> 349 <filter>assembly['type'] == 'genome' and 'pdf' in output_files</filter>
339 </data> 350 </data>
340 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/quast.log"> 351 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/quast.log">
341 <filter>'log' in output_files</filter> 352 <filter>assembly['type'] == 'genome' and 'log' in output_files</filter>
353 </data>
354 <data name="log_meta" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outputdir/metaquast.log">
355 <filter>assembly['type'] == 'metagenome' and 'log' in output_files</filter>
342 </data> 356 </data>
343 <data name="mis_ass" format="tabular" label="${tool.name} on ${on_string}: Misassemblies report" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt"> 357 <data name="mis_ass" format="tabular" label="${tool.name} on ${on_string}: Misassemblies report" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt">
344 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter> 358 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true'</filter>
345 <filter>'tabular' in output_files</filter> 359 <filter>'tabular' in output_files</filter>
346 </data> 360 </data>
352 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['k_mer']['k_mer_stats'] != ''</filter> 366 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['k_mer']['k_mer_stats'] != ''</filter>
353 <filter>'tabular' in output_files</filter> 367 <filter>'tabular' in output_files</filter>
354 </data> 368 </data>
355 <data name="circos_output" format="png" from_work_dir="outputdir/circos/circos.png" label="${tool.name} on ${on_string}: Circos plot"> 369 <data name="circos_output" format="png" from_work_dir="outputdir/circos/circos.png" label="${tool.name} on ${on_string}: Circos plot">
356 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['circos']</filter> 370 <filter>assembly['type'] == 'genome' and assembly['ref']['use_ref'] == 'true' and assembly['ref']['circos']</filter>
371 </data>
372 <collection name="metrics_tabular" type="list" label="${tool.name} on ${on_string}: Tabular reports for key metrics" >
373 <discover_datasets pattern="(?P&lt;designation&gt;.+).tsv" directory="outputdir/summary/TSV/" format="tabular"/>
374 <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
375 </collection>
376 <collection name="metrics_pdf" type="list" label="${tool.name} on ${on_string}: PDF reports for key metrics" >
377 <discover_datasets pattern="(?P&lt;designation&gt;.+).pdf" directory="outputdir/summary/PDF/" format="pdf"/>
378 <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
379 </collection>
380 <data name="krona" format="html" label="${tool.name} on ${on_string}: Krona chart" from_work_dir="outputdir/krona_charts/*.html">
381 <filter>assembly['type'] == 'metagenome' and assembly['ref']['origin'] == 'none' and 'krona' in output_files</filter>
357 </data> 382 </data>
358 </outputs> 383 </outputs>
359 <tests> 384 <tests>
360 <!-- Test 01: reference, genes annotations and operon coordinates --> 385 <!-- Test 01: reference, genes annotations and operon coordinates -->
361 <test expect_num_outputs="2"> 386 <test expect_num_outputs="2">
443 </conditional> 468 </conditional>
444 </conditional> 469 </conditional>
445 <param name="output_files" value="html,pdf,tabular,log"/> 470 <param name="output_files" value="html,pdf,tabular,log"/>
446 <output name="report_html" file="test2_report.html" ftype="html" compare="sim_size"/> 471 <output name="report_html" file="test2_report.html" ftype="html" compare="sim_size"/>
447 <output name="report_pdf" file="test2_report.pdf" ftype="pdf" compare="sim_size"/> 472 <output name="report_pdf" file="test2_report.pdf" ftype="pdf" compare="sim_size"/>
448 <output name="quast_tabular" file="test2_report.tab" ftype="tabular"/> 473 <output name="report_tabular" file="test2_report.tab" ftype="tabular"/>
449 <output name="log" file="test2.log" ftype="txt" compare="sim_size"/> 474 <output name="log" file="test2.log" ftype="txt" compare="sim_size"/>
450 <output name="mis_ass" file="test2_missasemblies.tab" ftype="tabular"/> 475 <output name="mis_ass" file="test2_missasemblies.tab" ftype="tabular"/>
451 <output name="unalign" file="test2_unaligned.tab" ftype="tabular"/> 476 <output name="unalign" file="test2_unaligned.tab" ftype="tabular"/>
452 <output name="kmers" file="test2_kmers.tab" ftype="tabular"/> 477 <output name="kmers" file="test2_kmers.tab" ftype="tabular"/>
453 <output name="circos_output" file="test2_circos.png" ftype="png" compare="sim_size"/> 478 <output name="circos_output" file="test2_circos.png" ftype="png" compare="sim_size"/>
532 <param name="extensive_mis_size" value="1000"/> 557 <param name="extensive_mis_size" value="1000"/>
533 <param name="scaffold_gap_max_size" value="1000"/> 558 <param name="scaffold_gap_max_size" value="1000"/>
534 <param name="unaligned_part_size" value="500"/> 559 <param name="unaligned_part_size" value="500"/>
535 <param name="skip_unaligned_mis_contigs" value="-"/> 560 <param name="skip_unaligned_mis_contigs" value="-"/>
536 </section> 561 </section>
537 <param name="output_files" value="tabular"/> 562 <param name="output_files" value="log"/>
538 <output name="quast_tabular" file="test4.tab" ftype="tabular"/> 563 <output name="log_meta" ftype="txt">
564 <assert_contents>
565 <has_text text="Reference genomes are not found" />
566 </assert_contents>
567 </output>
539 </test> 568 </test>
540 <!-- Test 05: FASTQ read files --> 569 <!-- Test 05: FASTQ read files -->
541 <test expect_num_outputs="3"> 570 <test expect_num_outputs="3">
542 <conditional name="in"> 571 <conditional name="in">
543 <param name="custom" value="true"/> 572 <param name="custom" value="true"/>
564 <section name="alignments"> 593 <section name="alignments">
565 <param name="upper_bound_assembly" value="true"/> 594 <param name="upper_bound_assembly" value="true"/>
566 <param name="upper_bound_min_con" value="1"/> 595 <param name="upper_bound_min_con" value="1"/>
567 </section> 596 </section>
568 <param name="output_files" value="tabular"/> 597 <param name="output_files" value="tabular"/>
569 <output name="quast_tabular" file="test5.tab" ftype="tabular"/> 598 <output name="report_tabular" file="test5.tab" ftype="tabular"/>
570 <output name="mis_ass" file="test5_missasemblies.tab" ftype="tabular"/> 599 <output name="mis_ass" file="test5_missasemblies.tab" ftype="tabular"/>
571 <output name="unalign" file="test5_unaligned.tab" ftype="tabular"/> 600 <output name="unalign" file="test5_unaligned.tab" ftype="tabular"/>
572 </test> 601 </test>
573 <!-- Test 6: FASTQ.gz read files --> 602 <!-- Test 06: FASTQ.gz read files -->
574 <test expect_num_outputs="1"> 603 <test expect_num_outputs="1">
575 <conditional name="in"> 604 <conditional name="in">
576 <param name="custom" value="true"/> 605 <param name="custom" value="true"/>
577 <repeat name="inputs"> 606 <repeat name="inputs">
578 <param name="input" value="contigs1.fna"/> 607 <param name="input" value="contigs1.fna"/>
586 <conditional name="reads"> 615 <conditional name="reads">
587 <param name="reads_option" value="single"/> 616 <param name="reads_option" value="single"/>
588 <param name="input_1" value="pacbio_01.fastq.gz,pacbio_02.fastq.gz"/> 617 <param name="input_1" value="pacbio_01.fastq.gz,pacbio_02.fastq.gz"/>
589 </conditional> 618 </conditional>
590 <param name="output_files" value="tabular"/> 619 <param name="output_files" value="tabular"/>
591 <output name="quast_tabular" file="test6.tab" ftype="tabular"/> 620 <output name="report_tabular" file="test6.tab" ftype="tabular"/>
592 </test> 621 </test>
593 <!-- Test 7: FASTA.gz read files --> 622 <!-- Test 07: FASTA.gz read files -->
594 <test expect_num_outputs="1"> 623 <test expect_num_outputs="1">
595 <conditional name="in"> 624 <conditional name="in">
596 <param name="custom" value="true"/> 625 <param name="custom" value="true"/>
597 <repeat name="inputs"> 626 <repeat name="inputs">
598 <param name="input" value="contigs1.fna"/> 627 <param name="input" value="contigs1.fna"/>
606 <conditional name="reads"> 635 <conditional name="reads">
607 <param name="reads_option" value="single"/> 636 <param name="reads_option" value="single"/>
608 <param name="input_1" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> 637 <param name="input_1" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
609 </conditional> 638 </conditional>
610 <param name="output_files" value="tabular"/> 639 <param name="output_files" value="tabular"/>
611 <output name="quast_tabular" file="test7.tab" ftype="tabular"/> 640 <output name="report_tabular" file="test7.tab" ftype="tabular"/>
641 </test>
642 <!-- Test 08: metagenomics all tab outputs-->
643 <test expect_num_outputs="3">
644 <conditional name="in">
645 <param name="custom" value="false"/>
646 <param name="inputs" value="test8.fasta"/>
647 </conditional>
648 <conditional name="assembly">
649 <param name="type" value="metagenome"/>
650 <conditional name="ref">
651 <param name="origin" value="none"/>
652 </conditional>
653 </conditional>
654 <param name="min_contig" value="500"/>
655 <param name="split_scaffolds" value="false"/>
656 <param name="large" value="false"/>
657 <section name="genes">
658 <conditional name="gene_finding">
659 <param name="tool" value="none"/>
660 </conditional>
661 <param name="rna_finding" value="false"/>
662 <param name="conserved_genes_finding" value="false"/>
663 </section>
664 <section name="alignments">
665 <param name="use_all_alignments" value="false"/>
666 <param name="min_alignment" value="65"/>
667 <param name="min_identity" value="95.0"/>
668 <param name="ambiguity_usage" value="one"/>
669 <param name="ambiguity_score" value="0.99"/>
670 <param name="fragmented" value="false"/>
671 </section>
672 <section name="advanced">
673 <param name="contig_thresholds" value="0,1000"/>
674 <param name="strict_NA" value="false"/>
675 <param name="extensive_mis_size" value="1000"/>
676 <param name="scaffold_gap_max_size" value="1000"/>
677 <param name="unaligned_part_size" value="500"/>
678 <param name="skip_unaligned_mis_contigs" value="-"/>
679 </section>
680 <param name="output_files" value="tabular,summary"/>
681 <output name="report_tabular_meta" ftype="tabular">
682 <assert_contents>
683 <has_text text="contigs (>= 0 bp)" />
684 </assert_contents>
685 </output>
686 <output_collection name="metrics_tabular" type="list" count="14"/>
687 <output_collection name="metrics_pdf" type="list" count="15"/>
688 </test>
689 <!-- Test 09: metagenomics log, html and krona outputs-->
690 <test expect_num_outputs="4">
691 <conditional name="in">
692 <param name="custom" value="false"/>
693 <param name="inputs" value="test8.fasta"/>
694 </conditional>
695 <conditional name="assembly">
696 <param name="type" value="metagenome"/>
697 <conditional name="ref">
698 <param name="origin" value="none"/>
699 </conditional>
700 </conditional>
701 <param name="min_contig" value="500"/>
702 <param name="split_scaffolds" value="false"/>
703 <param name="large" value="false"/>
704 <section name="genes">
705 <conditional name="gene_finding">
706 <param name="tool" value="none"/>
707 </conditional>
708 <param name="rna_finding" value="false"/>
709 <param name="conserved_genes_finding" value="false"/>
710 </section>
711 <section name="alignments">
712 <param name="use_all_alignments" value="false"/>
713 <param name="min_alignment" value="65"/>
714 <param name="min_identity" value="95.0"/>
715 <param name="ambiguity_usage" value="all"/>
716 <param name="ambiguity_score" value="0.99"/>
717 <param name="fragmented" value="false"/>
718 </section>
719 <section name="advanced">
720 <param name="contig_thresholds" value="0,1000"/>
721 <param name="strict_NA" value="false"/>
722 <param name="extensive_mis_size" value="1000"/>
723 <param name="scaffold_gap_max_size" value="1000"/>
724 <param name="unaligned_part_size" value="500"/>
725 <param name="skip_unaligned_mis_contigs" value="-"/>
726 </section>
727 <param name="output_files" value="html,log,krona"/>
728 <output name="report_html" ftype="html">
729 <assert_contents>
730 <has_text text="Vibrio_parahaemolyticus" />
731 </assert_contents>
732 </output>
733 <output name="report_html_meta" ftype="html">
734 <assert_contents>
735 <has_text text="Total length (>= 1000 bp)" />
736 </assert_contents>
737 </output>
738 <output name="log_meta" ftype="txt">
739 <assert_contents>
740 <has_text text="Vibrio_parahaemolyticus | successfully downloaded" />
741 </assert_contents>
742 </output>
743 <output name="krona" ftype="html">
744 <assert_contents>
745 <has_text text="Vibrio_parahaemolyticus" />
746 </assert_contents>
747 </output>
612 </test> 748 </test>
613 </tests> 749 </tests>
614 <help> 750 <help>
615 <![CDATA[ 751 <![CDATA[
616 **What it does** 752 **What it does**
620 If you have one or multiple genome assemblies, you can assess their quality with Quast. It works with or without reference genome. If you are new to Quast, start by reading its `manual page <http://quast.sourceforge.net/docs/manual.html>`_. 756 If you have one or multiple genome assemblies, you can assess their quality with Quast. It works with or without reference genome. If you are new to Quast, start by reading its `manual page <http://quast.sourceforge.net/docs/manual.html>`_.
621 757
622 **Using Quast without reference** 758 **Using Quast without reference**
623 759
624 Without reference Quast can calculate a number of assembly related-metrics but cannot provide any information about potential misassemblies, inversions, translocations, etc. Suppose you have three assemblies produced by Unicycler corresponding to three different antibiotic treatments *car*, *pit*, and *cef* (these stand for carbenicillin, piperacillin, and cefsulodin, respectively). Evaluating them without reference will produce the following Quast outputs: 760 Without reference Quast can calculate a number of assembly related-metrics but cannot provide any information about potential misassemblies, inversions, translocations, etc. Suppose you have three assemblies produced by Unicycler corresponding to three different antibiotic treatments *car*, *pit*, and *cef* (these stand for carbenicillin, piperacillin, and cefsulodin, respectively). Evaluating them without reference will produce the following Quast outputs:
625 761
626 * Quast report in HTML format 762 * Quast report in HTML format
627 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file) 763 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
628 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format 764 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format
629 * Quast log (a file technical information about Quast tool execution) 765 * Quast log (a file technical information about Quast tool execution)
630 766