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comparison metaphlan.xml @ 6:2131d7dca455 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 08ec37116aab4268fdb93f175b60e50a0bbfafb2
author iuc
date Mon, 27 Feb 2023 07:01:00 +0000
parents 6dee4abadccb
children 1a6cdf55390f
comparison
equal deleted inserted replaced
5:6dee4abadccb 6:2131d7dca455
261 <param name="db_selector" type="select" label="Database with clade-specific marker genes"> 261 <param name="db_selector" type="select" label="Database with clade-specific marker genes">
262 <option value="cached" selected="true">Locally cached</option> 262 <option value="cached" selected="true">Locally cached</option>
263 <option value="history">From history</option> 263 <option value="history">From history</option>
264 </param> 264 </param>
265 <when value="cached"> 265 <when value="cached">
266 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select"> 266 <param name="cached_db" type="select" label="Cached database with clade-specific marker genes">
267 <options from_data_table="metaphlan_database"> 267 <options from_data_table="@IDX_DATA_TABLE@">
268 <validator message="No MetaPhlAn database is available" type="no_options" /> 268 <filter type="static_value" column="4" value="@IDX_VERSION@"/>
269 <validator message="No compatible MetaPhlAn database is available" type="no_options"/>
269 </options> 270 </options>
270 </param> 271 </param>
271 </when> 272 </when>
272 <when value="history"> 273 <when value="history">
273 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/> 274 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>
274 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/> 275 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associated to the database with clade-specific marker genes from history"/>
275 </when> 276 </when>
276 </conditional> 277 </conditional>
277 </section> 278 </section>
278 <section name="analysis" title="Analysis" expanded="true"> 279 <section name="analysis" title="Analysis" expanded="true">
279 <conditional name="analysis_type"> 280 <conditional name="analysis_type">
433 <not_has_text text="k__Bacteria"/> 434 <not_has_text text="k__Bacteria"/>
434 <not_has_text text="p__Actinobacteria"/> 435 <not_has_text text="p__Actinobacteria"/>
435 </assert_contents> 436 </assert_contents>
436 </output> 437 </output>
437 <output_collection name="levels" type="list" > 438 <output_collection name="levels" type="list" >
439
438 <element name="all" ftype="tabular"> 440 <element name="all" ftype="tabular">
439 <assert_contents> 441 <assert_contents>
440 <has_text text="class"/> 442 <has_text text="class"/>
441 <has_n_columns n="17"/> 443 <has_n_columns n="17"/>
442 <has_n_lines n="1"/> 444 <has_n_lines n="1"/>
443 </assert_contents> 445 </assert_contents>
444 </element> 446 </element>
447 <element name="class" ftype="tabular">
448 <assert_contents>
449 <has_text text="class_id"/>
450 <not_has_text text="phylum_id"/>
451 <has_n_columns n="3"/>
452 <has_n_lines n="1"/>
453 </assert_contents>
454 </element>
455 <element name="family" ftype="tabular">
456 <assert_contents>
457 <has_text text="family_id"/>
458 <not_has_text text="order"/>
459 <has_n_columns n="3"/>
460 <has_n_lines n="1"/>
461 </assert_contents>
462 </element>
463 <element name="genus" ftype="tabular">
464 <assert_contents>
465 <has_text text="genus_id"/>
466 <not_has_text text="family"/>
467 <has_n_columns n="3"/>
468 <has_n_lines n="1"/>
469 </assert_contents>
470 </element>
445 <element name="kingdom" ftype="tabular"> 471 <element name="kingdom" ftype="tabular">
446 <assert_contents> 472 <assert_contents>
447 <has_text text="kingdom_id"/> 473 <has_text text="kingdom_id"/>
474 <has_n_columns n="3"/>
475 <has_n_lines n="1"/>
476 </assert_contents>
477 </element>
478 <element name="order" ftype="tabular">
479 <assert_contents>
480 <has_text text="order_id"/>
481 <not_has_text text="class_id"/>
448 <has_n_columns n="3"/> 482 <has_n_columns n="3"/>
449 <has_n_lines n="1"/> 483 <has_n_lines n="1"/>
450 </assert_contents> 484 </assert_contents>
451 </element> 485 </element>
452 <element name="phylum" ftype="tabular"> 486 <element name="phylum" ftype="tabular">
453 <assert_contents> 487 <assert_contents>
454 <has_text text="phylum_id"/> 488 <has_text text="phylum_id"/>
455 <not_has_text text="kingdom_id"/> 489 <not_has_text text="kingdom_id"/>
456 <has_n_columns n="3"/>
457 <has_n_lines n="1"/>
458 </assert_contents>
459 </element>
460 <element name="class" ftype="tabular">
461 <assert_contents>
462 <has_text text="class_id"/>
463 <not_has_text text="phylum_id"/>
464 <has_n_columns n="3"/>
465 <has_n_lines n="1"/>
466 </assert_contents>
467 </element>
468 <element name="order" ftype="tabular">
469 <assert_contents>
470 <has_text text="order_id"/>
471 <not_has_text text="class_id"/>
472 <has_n_columns n="3"/>
473 <has_n_lines n="1"/>
474 </assert_contents>
475 </element>
476 <element name="family" ftype="tabular">
477 <assert_contents>
478 <has_text text="family_id"/>
479 <not_has_text text="order"/>
480 <has_n_columns n="3"/>
481 <has_n_lines n="1"/>
482 </assert_contents>
483 </element>
484 <element name="genus" ftype="tabular">
485 <assert_contents>
486 <has_text text="genus_id"/>
487 <not_has_text text="family"/>
488 <has_n_columns n="3"/> 490 <has_n_columns n="3"/>
489 <has_n_lines n="1"/> 491 <has_n_lines n="1"/>
490 </assert_contents> 492 </assert_contents>
491 </element> 493 </element>
492 <element name="species" ftype="tabular"> 494 <element name="species" ftype="tabular">
586 <has_text text="Gammaproteobacteria"/> 588 <has_text text="Gammaproteobacteria"/>
587 <has_text text="Corynebacterium accolens"/> 589 <has_text text="Corynebacterium accolens"/>
588 <has_n_columns n="17"/> 590 <has_n_columns n="17"/>
589 </assert_contents> 591 </assert_contents>
590 </element> 592 </element>
593 <element name="class" ftype="tabular">
594 <assert_contents>
595 <has_text text="class_id"/>
596 <not_has_text text="phylum_id"/>
597 <has_text text="Actinobacteria"/>
598 <has_n_columns n="3"/>
599 </assert_contents>
600 </element>
601 <element name="family" ftype="tabular">
602 <assert_contents>
603 <has_text text="family_id"/>
604 <not_has_text text="order"/>
605 <has_text text="Propionibacteriaceae"/>
606 <has_n_columns n="3"/>
607 </assert_contents>
608 </element>
609 <element name="genus" ftype="tabular">
610 <assert_contents>
611 <has_text text="genus_id"/>
612 <not_has_text text="family"/>
613 <has_text text="Cutibacterium"/>
614 <has_n_columns n="3"/>
615 </assert_contents>
616 </element>
591 <element name="kingdom" ftype="tabular"> 617 <element name="kingdom" ftype="tabular">
592 <assert_contents> 618 <assert_contents>
593 <has_text text="kingdom_id"/> 619 <has_text text="kingdom_id"/>
594 <has_text text="Bacteria"/> 620 <has_text text="Bacteria"/>
621 <has_n_columns n="3"/>
622 </assert_contents>
623 </element>
624 <element name="order" ftype="tabular">
625 <assert_contents>
626 <has_text text="order_id"/>
627 <not_has_text text="class_id"/>
628 <has_text text="Propionibacteriales"/>
595 <has_n_columns n="3"/> 629 <has_n_columns n="3"/>
596 </assert_contents> 630 </assert_contents>
597 </element> 631 </element>
598 <element name="phylum" ftype="tabular"> 632 <element name="phylum" ftype="tabular">
599 <assert_contents> 633 <assert_contents>
600 <has_text text="phylum_id"/> 634 <has_text text="phylum_id"/>
601 <not_has_text text="kingdom_id"/> 635 <not_has_text text="kingdom_id"/>
602 <has_text text="Firmicutes"/> 636 <has_text text="Firmicutes"/>
603 <has_n_columns n="3"/>
604 </assert_contents>
605 </element>
606 <element name="class" ftype="tabular">
607 <assert_contents>
608 <has_text text="class_id"/>
609 <not_has_text text="phylum_id"/>
610 <has_text text="Actinobacteria"/>
611 <has_n_columns n="3"/>
612 </assert_contents>
613 </element>
614 <element name="order" ftype="tabular">
615 <assert_contents>
616 <has_text text="order_id"/>
617 <not_has_text text="class_id"/>
618 <has_text text="Propionibacteriales"/>
619 <has_n_columns n="3"/>
620 </assert_contents>
621 </element>
622 <element name="family" ftype="tabular">
623 <assert_contents>
624 <has_text text="family_id"/>
625 <not_has_text text="order"/>
626 <has_text text="Propionibacteriaceae"/>
627 <has_n_columns n="3"/>
628 </assert_contents>
629 </element>
630 <element name="genus" ftype="tabular">
631 <assert_contents>
632 <has_text text="genus_id"/>
633 <not_has_text text="family"/>
634 <has_text text="Cutibacterium"/>
635 <has_n_columns n="3"/> 637 <has_n_columns n="3"/>
636 </assert_contents> 638 </assert_contents>
637 </element> 639 </element>
638 <element name="species" ftype="tabular"> 640 <element name="species" ftype="tabular">
639 <assert_contents> 641 <assert_contents>
986 <has_text text="Gammaproteobacteria"/> 988 <has_text text="Gammaproteobacteria"/>
987 <has_text text="Corynebacterium accolens"/> 989 <has_text text="Corynebacterium accolens"/>
988 <has_n_columns n="9"/> 990 <has_n_columns n="9"/>
989 </assert_contents> 991 </assert_contents>
990 </element> 992 </element>
993 <element name="class" ftype="tabular">
994 <assert_contents>
995 <has_text text="class"/>
996 <has_text text="Actinobacteria"/>
997 <has_n_columns n="2"/>
998 </assert_contents>
999 </element>
1000 <element name="family" ftype="tabular">
1001 <assert_contents>
1002 <has_text text="family"/>
1003 <has_text text="Propionibacteriaceae"/>
1004 <has_n_columns n="2"/>
1005 </assert_contents>
1006 </element>
1007 <element name="genus" ftype="tabular">
1008 <assert_contents>
1009 <has_text text="genus"/>
1010 <has_text text="Cutibacterium"/>
1011 <has_n_columns n="2"/>
1012 </assert_contents>
1013 </element>
991 <element name="kingdom" ftype="tabular"> 1014 <element name="kingdom" ftype="tabular">
992 <assert_contents> 1015 <assert_contents>
993 <has_text text="kingdom"/> 1016 <has_text text="kingdom"/>
994 <has_text text="Bacteria"/> 1017 <has_text text="Bacteria"/>
995 <has_n_columns n="2"/> 1018 <has_n_columns n="2"/>
996 </assert_contents> 1019 </assert_contents>
997 </element> 1020 </element>
998 <element name="phylum" ftype="tabular">
999 <assert_contents>
1000 <has_text text="phylum"/>
1001 <has_text text="Firmicutes"/>
1002 <has_n_columns n="2"/>
1003 </assert_contents>
1004 </element>
1005 <element name="class" ftype="tabular">
1006 <assert_contents>
1007 <has_text text="class"/>
1008 <has_text text="Actinobacteria"/>
1009 <has_n_columns n="2"/>
1010 </assert_contents>
1011 </element>
1012 <element name="order" ftype="tabular"> 1021 <element name="order" ftype="tabular">
1013 <assert_contents> 1022 <assert_contents>
1014 <has_text text="order"/> 1023 <has_text text="order"/>
1015 <has_text text="Propionibacteriales"/> 1024 <has_text text="Propionibacteriales"/>
1016 <has_n_columns n="2"/> 1025 <has_n_columns n="2"/>
1017 </assert_contents> 1026 </assert_contents>
1018 </element> 1027 </element>
1019 <element name="family" ftype="tabular"> 1028 <element name="phylum" ftype="tabular">
1020 <assert_contents> 1029 <assert_contents>
1021 <has_text text="family"/> 1030 <has_text text="phylum"/>
1022 <has_text text="Propionibacteriaceae"/> 1031 <has_text text="Firmicutes"/>
1023 <has_n_columns n="2"/>
1024 </assert_contents>
1025 </element>
1026 <element name="genus" ftype="tabular">
1027 <assert_contents>
1028 <has_text text="genus"/>
1029 <has_text text="Cutibacterium"/>
1030 <has_n_columns n="2"/> 1032 <has_n_columns n="2"/>
1031 </assert_contents> 1033 </assert_contents>
1032 </element> 1034 </element>
1033 <element name="species" ftype="tabular"> 1035 <element name="species" ftype="tabular">
1034 <assert_contents> 1036 <assert_contents>