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comparison metaphlan.xml @ 1:b89b0765695d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 2b87bc7417360e2b2c9ec0605d475909f6f0482f"
author iuc
date Mon, 17 May 2021 20:10:24 +0000
parents f5df500fcc3c
children a92a632c4d9b
comparison
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0:f5df500fcc3c 1:b89b0765695d
1 <tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>to profile the composition of microbial communities</description> 2 <description>to profile the composition of microbial communities</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <xml name="tax_lev">
6 <conditional name="tax_lev">
7 <param argument="--tax_lev" type="select" label="Taxonomic level for the relative abundance output">
8 <option value="a" selected="true">All taxonomic levels</option>
9 <option value="k">Kingdoms only</option>
10 <option value="p">Phyla only</option>
11 <option value="c">Classes only</option>
12 <option value="o">Orders only</option>
13 <option value="f">Families only</option>
14 <option value="g">Genera only</option>
15 <option value="s">Species only</option>
16 </param>
17 <when value="a">
18 <param name="split_levels" type='boolean' checked="false" truevalue='true' falsevalue='false'
19 label="Generate a report for each taxonomic level?" help="It will be in addition to the default output"/>
20 </when>
21 <when value="k"/>
22 <when value="p"/>
23 <when value="c"/>
24 <when value="o"/>
25 <when value="f"/>
26 <when value="g"/>
27 <when value="s"/>
28 </conditional>
29 </xml>
30 <token name="@FILE_FORMATS@">fastq,fastq.gz,fastq.bz2,fasta,fasta.gz,fasta.bz2</token>
5 </macros> 31 </macros>
6 <expand macro="edam_ontology"/> 32 <expand macro="edam_ontology"/>
7 <expand macro="requirements"/> 33 <expand macro="requirements"/>
8 <version_command>metaphlan -v</version_command> 34 <version_command>metaphlan -v</version_command>
9 <command detect_errors="aggressive"><![CDATA[ 35 <command detect_errors="aggressive"><![CDATA[
108 --bowtie2db 'ref_db/' 134 --bowtie2db 'ref_db/'
109 --index 'custom_db' 135 --index 'custom_db'
110 #end if 136 #end if
111 -t '$analysis.analysis_type.t' 137 -t '$analysis.analysis_type.t'
112 #if $analysis.analysis_type.t == "rel_ab" or $analysis.analysis_type.t == "rel_ab_w_read_stats" 138 #if $analysis.analysis_type.t == "rel_ab" or $analysis.analysis_type.t == "rel_ab_w_read_stats"
113 --tax_lev '$analysis.analysis_type.tax_lev' 139 --tax_lev '$analysis.analysis_type.tax_lev.tax_lev'
114 #else if $analysis.analysis_type.t == "clade_specific_strain_tracker" 140 #else if $analysis.analysis_type.t == "clade_specific_strain_tracker"
115 --clade '$analysis.analysis_type.clade' 141 --clade '$analysis.analysis_type.clade'
116 #if str($analysis.analysis_type.min_ab) != '' 142 #if str($analysis.analysis_type.min_ab) != ''
117 --min_ab $analysis.analysis_type.min_ab 143 --min_ab $analysis.analysis_type.min_ab
118 #end if 144 #end if
156 --nproc \${GALAXY_SLOTS:-4} 182 --nproc \${GALAXY_SLOTS:-4}
157 183
158 #if $inputs.in.selector == "raw" 184 #if $inputs.in.selector == "raw"
159 && 185 &&
160 mv 'bowtie2out' '$bowtie2out' 186 mv 'bowtie2out' '$bowtie2out'
187 #end if
188
189 #if $analysis.analysis_type.tax_lev.tax_lev == 'a' and $analysis.analysis_type.tax_lev.split_levels
190 &&
191 mkdir 'split_levels'
192 &&
193 python '$__tool_directory__/formatoutput.py'
194 split_levels
195 --metaphlan_output '$output_file'
196 --outdir 'split_levels'
197 $out.legacy_output
198 &&
199 ls split_levels
200 #end if
201
202 #if $out.krona_output
203 &&
204 python '$__tool_directory__/formatoutput.py'
205 format_for_krona
206 --metaphlan_output '$output_file'
207 --krona_output '$krona_output_file'
161 #end if 208 #end if
162 ]]></command> 209 ]]></command>
163 <inputs> 210 <inputs>
164 <section name="inputs" title="Inputs" expanded="true"> 211 <section name="inputs" title="Inputs" expanded="true">
165 <conditional name="in"> 212 <conditional name="in">
292 label="Old MetaPhlAn2 two columns output?"/> 339 label="Old MetaPhlAn2 two columns output?"/>
293 <param argument="--CAMI_format_output" type='boolean' checked="false" truevalue='--CAMI_format_output' falsevalue='' 340 <param argument="--CAMI_format_output" type='boolean' checked="false" truevalue='--CAMI_format_output' falsevalue=''
294 label="Report the profiling using the CAMI output format?"/> 341 label="Report the profiling using the CAMI output format?"/>
295 <param argument="--unknown_estimation" type='boolean' checked="false" truevalue='--unknown_estimation' falsevalue='' 342 <param argument="--unknown_estimation" type='boolean' checked="false" truevalue='--unknown_estimation' falsevalue=''
296 label="Scale relative abundances to the number of reads mapping to known clades in order to estimate unknowness?"/> 343 label="Scale relative abundances to the number of reads mapping to known clades in order to estimate unknowness?"/>
344 <param name="krona_output" type='boolean' checked="false" truevalue='true' falsevalue='false' label="Output for Krona?"/>
297 </section> 345 </section>
298 </inputs> 346 </inputs>
299 <outputs> 347 <outputs>
300 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances" /> 348 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances" />
301 <data name="bowtie2out" format="tabular" label="${tool.name} on ${on_string}: Bowtie2 output"> 349 <data name="bowtie2out" format="tabular" label="${tool.name} on ${on_string}: Bowtie2 output">
303 </data> 351 </data>
304 <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file"> 352 <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file">
305 <filter>inputs['in']['selector'] == "raw"</filter> 353 <filter>inputs['in']['selector'] == "raw"</filter>
306 </data> 354 </data>
307 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" /> 355 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" />
356 <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels" >
357 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="split_levels/" format="tabular"/>
358 <filter>analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter>
359 </collection>
360 <data name="krona_output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances for Krona">
361 <filter>out['krona_output']</filter>
362 </data>
308 </outputs> 363 </outputs>
309 <tests> 364 <tests>
310 <test expect_num_outputs="4"> 365 <test expect_num_outputs="6">
311 <section name="inputs"> 366 <section name="inputs">
312 <conditional name="in"> 367 <conditional name="in">
313 <param name="selector" value="raw"/> 368 <param name="selector" value="raw"/>
314 <conditional name="raw_in"> 369 <conditional name="raw_in">
315 <!-- Single GZ file --> 370 <!-- Single GZ file -->
327 <param name="db_selector" value="cached"/> 382 <param name="db_selector" value="cached"/>
328 <param name="cached_db" value="test-db-20210409"/> 383 <param name="cached_db" value="test-db-20210409"/>
329 </conditional> 384 </conditional>
330 </section> 385 </section>
331 <section name="analysis"> 386 <section name="analysis">
387 <conditional name="analysis_type">
388 <param name="t" value="rel_ab"/>
389 <conditional name="tax_lev">
390 <param name="tax_lev" value="a"/>
391 <param name="split_levels" value="true"/>
392 </conditional>
393 </conditional>
332 <param name="min_cu_len" value="2000"/> 394 <param name="min_cu_len" value="2000"/>
333 <param name="organism_profiling" value="add_viruses"/> 395 <param name="organism_profiling" value="add_viruses"/>
334 <param name="stat" value="avg_g"/> 396 <param name="stat" value="avg_g"/>
335 <param name="stat_q" value="0.2"/> 397 <param name="stat_q" value="0.2"/>
336 <param name="perc_nonzero" value="0.33"/> 398 <param name="perc_nonzero" value="0.33"/>
341 <param name="sample_id" value="Metaphlan_Analysis"/> 403 <param name="sample_id" value="Metaphlan_Analysis"/>
342 <param name="use_group_representative" value="false"/> 404 <param name="use_group_representative" value="false"/>
343 <param name="legacy_output" value="false"/> 405 <param name="legacy_output" value="false"/>
344 <param name="CAMI_format_output" value="false"/> 406 <param name="CAMI_format_output" value="false"/>
345 <param name="unknown_estimation" value="false"/> 407 <param name="unknown_estimation" value="false"/>
408 <param name="krona_output" value="true"/>
346 </section> 409 </section>
347 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 410 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
348 <assert_contents> 411 <assert_contents>
349 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 412 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
350 </assert_contents> 413 </assert_contents>
361 </assert_contents> 424 </assert_contents>
362 </output> 425 </output>
363 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size"> 426 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
364 <assert_contents> 427 <assert_contents>
365 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/> 428 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
429 </assert_contents>
430 </output>
431 <output_collection name="levels" type="list" >
432 <element name="all" ftype="tabular">
433 <assert_contents>
434 <has_text text="Gammaproteobacteria"/>
435 <has_text text="Corynebacterium accolens"/>
436 <has_n_columns n="17"/>
437 </assert_contents>
438 </element>
439 <element name="kingdom" ftype="tabular">
440 <assert_contents>
441 <has_text text="kingdom_id"/>
442 <has_text text="Bacteria"/>
443 <has_n_columns n="3"/>
444 </assert_contents>
445 </element>
446 <element name="phylum" ftype="tabular">
447 <assert_contents>
448 <has_text text="phylum_id"/>
449 <not_has_text text="kingdom_id"/>
450 <has_text text="Firmicutes"/>
451 <has_n_columns n="3"/>
452 </assert_contents>
453 </element>
454 <element name="class" ftype="tabular">
455 <assert_contents>
456 <has_text text="class_id"/>
457 <not_has_text text="phylum_id"/>
458 <has_text text="Actinobacteria"/>
459 <has_n_columns n="3"/>
460 </assert_contents>
461 </element>
462 <element name="order" ftype="tabular">
463 <assert_contents>
464 <has_text text="order_id"/>
465 <not_has_text text="class_id"/>
466 <has_text text="Propionibacteriales"/>
467 <has_n_columns n="3"/>
468 </assert_contents>
469 </element>
470 <element name="family" ftype="tabular">
471 <assert_contents>
472 <has_text text="family_id"/>
473 <not_has_text text="order"/>
474 <has_text text="Propionibacteriaceae"/>
475 <has_n_columns n="3"/>
476 </assert_contents>
477 </element>
478 <element name="genus" ftype="tabular">
479 <assert_contents>
480 <has_text text="genus_id"/>
481 <not_has_text text="family"/>
482 <has_text text="Cutibacterium"/>
483 <has_n_columns n="3"/>
484 </assert_contents>
485 </element>
486 <element name="species" ftype="tabular">
487 <assert_contents>
488 <has_text text="species_id"/>
489 <not_has_text text="genus"/>
490 <has_text text="Corynebacterium accolens"/>
491 <has_n_columns n="3"/>
492 </assert_contents>
493 </element>
494 <element name="strains" ftype="tabular">
495 <assert_contents>
496 <has_text text="strains_id"/>
497 <not_has_text text="species_id"/>
498 <has_n_columns n="3"/>
499 </assert_contents>
500 </element>
501 </output_collection>
502 <output name="krona_output_file" ftype="tabular">
503 <assert_contents>
504 <not_has_text text="k__Bacteria"/>
505 <has_text text="Corynebacterium accolens"/>
506 <has_n_columns n="9"/>
366 </assert_contents> 507 </assert_contents>
367 </output> 508 </output>
368 </test> 509 </test>
369 <test expect_num_outputs="4"> 510 <test expect_num_outputs="4">
370 <section name="inputs"> 511 <section name="inputs">
387 <param name="bowtie2db" value="test-db.fasta"/> 528 <param name="bowtie2db" value="test-db.fasta"/>
388 <param name="mpa_pkl" value="test-db.json"/> 529 <param name="mpa_pkl" value="test-db.json"/>
389 </conditional> 530 </conditional>
390 </section> 531 </section>
391 <section name="analysis"> 532 <section name="analysis">
533 <conditional name="analysis_type">
534 <param name="t" value="rel_ab"/>
535 <conditional name="tax_lev">
536 <param name="tax_lev" value="a"/>
537 <param name="split_levels" value="false"/>
538 </conditional>
539 </conditional>
392 <param name="min_cu_len" value="2000"/> 540 <param name="min_cu_len" value="2000"/>
393 <param name="organism_profiling" value="add_viruses"/> 541 <param name="organism_profiling" value="add_viruses"/>
394 <param name="stat" value="avg_g"/> 542 <param name="stat" value="avg_g"/>
395 <param name="stat_q" value="0.2"/> 543 <param name="stat_q" value="0.2"/>
396 <param name="perc_nonzero" value="0.33"/> 544 <param name="perc_nonzero" value="0.33"/>
401 <param name="sample_id" value="Metaphlan_Analysis"/> 549 <param name="sample_id" value="Metaphlan_Analysis"/>
402 <param name="use_group_representative" value="false"/> 550 <param name="use_group_representative" value="false"/>
403 <param name="legacy_output" value="false"/> 551 <param name="legacy_output" value="false"/>
404 <param name="CAMI_format_output" value="false"/> 552 <param name="CAMI_format_output" value="false"/>
405 <param name="unknown_estimation" value="false"/> 553 <param name="unknown_estimation" value="false"/>
554 <param name="krona_output" value="false"/>
406 </section> 555 </section>
407 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 556 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
408 <assert_contents> 557 <assert_contents>
409 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 558 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
410 <has_text text="relative_abundance"/> 559 <has_text text="relative_abundance"/>
450 <param name="db_selector" value="cached"/> 599 <param name="db_selector" value="cached"/>
451 <param name="cached_db" value="test-db-20210409"/> 600 <param name="cached_db" value="test-db-20210409"/>
452 </conditional> 601 </conditional>
453 </section> 602 </section>
454 <section name="analysis"> 603 <section name="analysis">
604 <conditional name="analysis_type">
605 <param name="t" value="rel_ab"/>
606 <conditional name="tax_lev">
607 <param name="tax_lev" value="a"/>
608 <param name="split_levels" value="false"/>
609 </conditional>
610 </conditional>
455 <param name="min_cu_len" value="2000"/> 611 <param name="min_cu_len" value="2000"/>
456 <param name="organism_profiling" value="add_viruses"/> 612 <param name="organism_profiling" value="add_viruses"/>
457 <param name="stat" value="avg_g"/> 613 <param name="stat" value="avg_g"/>
458 <param name="stat_q" value="0.2"/> 614 <param name="stat_q" value="0.2"/>
459 <param name="perc_nonzero" value="0.33"/> 615 <param name="perc_nonzero" value="0.33"/>
464 <param name="sample_id" value="Metaphlan_Analysis"/> 620 <param name="sample_id" value="Metaphlan_Analysis"/>
465 <param name="use_group_representative" value="false"/> 621 <param name="use_group_representative" value="false"/>
466 <param name="legacy_output" value="false"/> 622 <param name="legacy_output" value="false"/>
467 <param name="CAMI_format_output" value="false"/> 623 <param name="CAMI_format_output" value="false"/>
468 <param name="unknown_estimation" value="false"/> 624 <param name="unknown_estimation" value="false"/>
625 <param name="krona_output" value="false"/>
469 </section> 626 </section>
470 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 627 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
471 <assert_contents> 628 <assert_contents>
472 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 629 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
473 <has_text text="relative_abundance"/> 630 <has_text text="relative_abundance"/>
504 <param name="db_selector" value="cached"/> 661 <param name="db_selector" value="cached"/>
505 <param name="cached_db" value="test-db-20210409"/> 662 <param name="cached_db" value="test-db-20210409"/>
506 </conditional> 663 </conditional>
507 </section> 664 </section>
508 <section name="analysis"> 665 <section name="analysis">
666 <conditional name="analysis_type">
667 <param name="t" value="rel_ab"/>
668 <conditional name="tax_lev">
669 <param name="tax_lev" value="a"/>
670 <param name="split_levels" value="false"/>
671 </conditional>
672 </conditional>
509 <param name="min_cu_len" value="2000"/> 673 <param name="min_cu_len" value="2000"/>
510 <param name="organism_profiling" value="add_viruses"/> 674 <param name="organism_profiling" value="add_viruses"/>
511 <param name="stat" value="avg_g"/> 675 <param name="stat" value="avg_g"/>
512 <param name="stat_q" value="0.2"/> 676 <param name="stat_q" value="0.2"/>
513 <param name="perc_nonzero" value="0.33"/> 677 <param name="perc_nonzero" value="0.33"/>
518 <param name="sample_id" value="Metaphlan_Analysis"/> 682 <param name="sample_id" value="Metaphlan_Analysis"/>
519 <param name="use_group_representative" value="false"/> 683 <param name="use_group_representative" value="false"/>
520 <param name="legacy_output" value="false"/> 684 <param name="legacy_output" value="false"/>
521 <param name="CAMI_format_output" value="false"/> 685 <param name="CAMI_format_output" value="false"/>
522 <param name="unknown_estimation" value="false"/> 686 <param name="unknown_estimation" value="false"/>
687 <param name="krona_output" value="false"/>
523 </section> 688 </section>
524 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 689 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
525 <assert_contents> 690 <assert_contents>
526 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 691 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
527 <has_text text="relative_abundance"/> 692 <has_text text="relative_abundance"/>
555 <section name="mapping"> 720 <section name="mapping">
556 <param name="bt2_ps" value="sensite"/> 721 <param name="bt2_ps" value="sensite"/>
557 <param name="min_mapq_val" value="5"/> 722 <param name="min_mapq_val" value="5"/>
558 </section> 723 </section>
559 <section name="analysis"> 724 <section name="analysis">
725 <conditional name="analysis_type">
726 <param name="t" value="rel_ab"/>
727 <conditional name="tax_lev">
728 <param name="tax_lev" value="a"/>
729 <param name="split_levels" value="false"/>
730 </conditional>
731 </conditional>
560 <param name="min_cu_len" value="2000"/> 732 <param name="min_cu_len" value="2000"/>
561 <param name="organism_profiling" value="add_viruses"/> 733 <param name="organism_profiling" value="add_viruses"/>
562 <param name="stat" value="avg_g"/> 734 <param name="stat" value="avg_g"/>
563 <param name="stat_q" value="0.2"/> 735 <param name="stat_q" value="0.2"/>
564 <param name="perc_nonzero" value="0.33"/> 736 <param name="perc_nonzero" value="0.33"/>
569 <param name="sample_id" value="Metaphlan_Analysis"/> 741 <param name="sample_id" value="Metaphlan_Analysis"/>
570 <param name="use_group_representative" value="false"/> 742 <param name="use_group_representative" value="false"/>
571 <param name="legacy_output" value="false"/> 743 <param name="legacy_output" value="false"/>
572 <param name="CAMI_format_output" value="false"/> 744 <param name="CAMI_format_output" value="false"/>
573 <param name="unknown_estimation" value="false"/> 745 <param name="unknown_estimation" value="false"/>
746 <param name="krona_output" value="false"/>
574 </section> 747 </section>
575 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 748 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
576 <assert_contents> 749 <assert_contents>
577 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 750 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
578 <has_text text="relative_abundance"/> 751 <has_text text="relative_abundance"/>
584 <assert_contents> 757 <assert_contents>
585 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/> 758 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
586 </assert_contents> 759 </assert_contents>
587 </output> 760 </output>
588 </test> 761 </test>
589 <test expect_num_outputs="4"> 762 <test expect_num_outputs="6">
590 <section name="inputs"> 763 <section name="inputs">
591 <conditional name="in"> 764 <conditional name="in">
592 <param name="selector" value="raw"/> 765 <param name="selector" value="raw"/>
593 <conditional name="raw_in"> 766 <conditional name="raw_in">
594 <!-- Single FASTA file --> 767 <!-- Single FASTA file -->
606 <param name="db_selector" value="cached"/> 779 <param name="db_selector" value="cached"/>
607 <param name="cached_db" value="test-db-20210409"/> 780 <param name="cached_db" value="test-db-20210409"/>
608 </conditional> 781 </conditional>
609 </section> 782 </section>
610 <section name="analysis"> 783 <section name="analysis">
784 <conditional name="analysis_type">
785 <param name="t" value="rel_ab"/>
786 <conditional name="tax_lev">
787 <param name="tax_lev" value="a"/>
788 <param name="split_levels" value="true"/>
789 </conditional>
790 </conditional>
611 <param name="min_cu_len" value="2000"/> 791 <param name="min_cu_len" value="2000"/>
612 <param name="organism_profiling" value="add_viruses"/> 792 <param name="organism_profiling" value="add_viruses"/>
613 <param name="stat" value="avg_g"/> 793 <param name="stat" value="avg_g"/>
614 <param name="stat_q" value="0.2"/> 794 <param name="stat_q" value="0.2"/>
615 <param name="perc_nonzero" value="0.33"/> 795 <param name="perc_nonzero" value="0.33"/>
621 <param name="sample_id" value="Metaphlan_Analysis"/> 801 <param name="sample_id" value="Metaphlan_Analysis"/>
622 <param name="use_group_representative" value="false"/> 802 <param name="use_group_representative" value="false"/>
623 <param name="legacy_output" value="true"/> 803 <param name="legacy_output" value="true"/>
624 <param name="CAMI_format_output" value="false"/> 804 <param name="CAMI_format_output" value="false"/>
625 <param name="unknown_estimation" value="false"/> 805 <param name="unknown_estimation" value="false"/>
806 <param name="krona_output" value="true"/>
626 </section> 807 </section>
627 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size"> 808 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size">
628 <assert_contents> 809 <assert_contents>
629 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 810 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
630 <has_text text="SampleID"/> 811 <has_text text="SampleID"/>
643 </assert_contents> 824 </assert_contents>
644 </output> 825 </output>
645 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size"> 826 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
646 <assert_contents> 827 <assert_contents>
647 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/> 828 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
829 </assert_contents>
830 </output>
831 <output_collection name="levels" type="list" >
832 <element name="all" ftype="tabular">
833 <assert_contents>
834 <has_text text="Gammaproteobacteria"/>
835 <has_text text="Corynebacterium accolens"/>
836 <has_n_columns n="9"/>
837 </assert_contents>
838 </element>
839 <element name="kingdom" ftype="tabular">
840 <assert_contents>
841 <has_text text="kingdom"/>
842 <has_text text="Bacteria"/>
843 <has_n_columns n="2"/>
844 </assert_contents>
845 </element>
846 <element name="phylum" ftype="tabular">
847 <assert_contents>
848 <has_text text="phylum"/>
849 <has_text text="Firmicutes"/>
850 <has_n_columns n="2"/>
851 </assert_contents>
852 </element>
853 <element name="class" ftype="tabular">
854 <assert_contents>
855 <has_text text="class"/>
856 <has_text text="Actinobacteria"/>
857 <has_n_columns n="2"/>
858 </assert_contents>
859 </element>
860 <element name="order" ftype="tabular">
861 <assert_contents>
862 <has_text text="order"/>
863 <has_text text="Propionibacteriales"/>
864 <has_n_columns n="2"/>
865 </assert_contents>
866 </element>
867 <element name="family" ftype="tabular">
868 <assert_contents>
869 <has_text text="family"/>
870 <has_text text="Propionibacteriaceae"/>
871 <has_n_columns n="2"/>
872 </assert_contents>
873 </element>
874 <element name="genus" ftype="tabular">
875 <assert_contents>
876 <has_text text="genus"/>
877 <has_text text="Cutibacterium"/>
878 <has_n_columns n="2"/>
879 </assert_contents>
880 </element>
881 <element name="species" ftype="tabular">
882 <assert_contents>
883 <has_text text="species"/>
884 <has_text text="Corynebacterium accolens"/>
885 <has_n_columns n="2"/>
886 </assert_contents>
887 </element>
888 <element name="strains" ftype="tabular">
889 <assert_contents>
890 <has_text text="strains"/>
891 <has_n_columns n="2"/>
892 </assert_contents>
893 </element>
894 </output_collection>
895 <output name="krona_output_file" ftype="tabular">
896 <assert_contents>
897 <not_has_text text="k__Bacteria"/>
898 <has_text text="Corynebacterium accolens"/>
899 <has_n_columns n="9"/>
648 </assert_contents> 900 </assert_contents>
649 </output> 901 </output>
650 </test> 902 </test>
651 </tests> 903 </tests>
652 <help><![CDATA[ 904 <help><![CDATA[