Mercurial > repos > iuc > usher_matutils

comparison matutils.xml @ 1:75e51e947a98 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit 59c78982b11e280895f2f51c25ada4613968dc79"
author iuc
date Sun, 19 Dec 2021 15:50:21 +0000
parents be59fa64e855
children
comparison
equal deleted inserted replaced
0:be59fa64e855 1:75e51e947a98
294 <filter>matutils_mode['options_mode'] == 'uncertainty' and 'find-neighborhood' in matutils_mode['uncertainty_options']</filter> 294 <filter>matutils_mode['options_mode'] == 'uncertainty' and 'find-neighborhood' in matutils_mode['uncertainty_options']</filter>
295 </data> 295 </data>
296 </outputs> 296 </outputs>
297 <tests> 297 <tests>
298 <test expect_num_outputs="3"> 298 <test expect_num_outputs="3">
299 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> 299 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
300 <conditional name="matutils_mode"> 300 <conditional name="matutils_mode">
301 <param name="options_mode" value="extract"/> 301 <param name="options_mode" value="extract"/>
302 <param name="resolve_polytomies" value="true"/> 302 <param name="resolve_polytomies" value="true"/>
303 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths"/> 303 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths"/>
304 <conditional name="operation_mode"> 304 <conditional name="operation_mode">
310 <output name="selected_samples" file="test_13_sample_names.txt" ftype="txt"/> 310 <output name="selected_samples" file="test_13_sample_names.txt" ftype="txt"/>
311 <output name="path_mutations" file="test_13_path_mutations.tabular" ftype="tabular"/> 311 <output name="path_mutations" file="test_13_path_mutations.tabular" ftype="tabular"/>
312 <output name="path_clades" file="test_13_path_clades.tabular" ftype="tabular"/> 312 <output name="path_clades" file="test_13_path_clades.tabular" ftype="tabular"/>
313 </test> 313 </test>
314 <test expect_num_outputs="5"> 314 <test expect_num_outputs="5">
315 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> 315 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
316 <conditional name="matutils_mode"> 316 <conditional name="matutils_mode">
317 <param name="options_mode" value="extract"/> 317 <param name="options_mode" value="extract"/>
318 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/> 318 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
319 <conditional name="operation_mode"> 319 <conditional name="operation_mode">
320 <param name="operation" value="samples"/> 320 <param name="operation" value="samples"/>
330 <has_size value="7219100" delta="300"/> 330 <has_size value="7219100" delta="300"/>
331 </assert_contents> 331 </assert_contents>
332 </output> 332 </output>
333 </test> 333 </test>
334 <test expect_num_outputs="4"> 334 <test expect_num_outputs="4">
335 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> 335 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
336 <conditional name="matutils_mode"> 336 <conditional name="matutils_mode">
337 <param name="options_mode" value="extract"/> 337 <param name="options_mode" value="extract"/>
338 <param name="outputs_extract" value="write-vcf-no-genotypes,write-mat,write-json,write-tree"/> 338 <param name="outputs_extract" value="write-vcf-no-genotypes,write-mat,write-json,write-tree"/>
339 <conditional name="operation_mode"> 339 <conditional name="operation_mode">
340 <param name="operation" value="mutation"/> 340 <param name="operation" value="mutation"/>
345 <output name="mutation_annotated" file="test_15_mutation_annotated_tree.pb" ftype="protobuf3"/> 345 <output name="mutation_annotated" file="test_15_mutation_annotated_tree.pb" ftype="protobuf3"/>
346 <output name="subtree_json" file="test_15_subtree.json" ftype="json"/> 346 <output name="subtree_json" file="test_15_subtree.json" ftype="json"/>
347 <output name="tree_newick" file="test_15_tree.nh" ftype="newick"/> 347 <output name="tree_newick" file="test_15_tree.nh" ftype="newick"/>
348 </test> 348 </test>
349 <test expect_num_outputs="3"> 349 <test expect_num_outputs="3">
350 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> 350 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
351 <conditional name="matutils_mode"> 351 <conditional name="matutils_mode">
352 <param name="options_mode" value="extract"/> 352 <param name="options_mode" value="extract"/>
353 <param name="outputs_extract" value="used-samples,sample-paths,write-vcf"/> 353 <param name="outputs_extract" value="used-samples,sample-paths,write-vcf"/>
354 <conditional name="operation_mode"> 354 <conditional name="operation_mode">
355 <param name="operation" value="clades"/> 355 <param name="operation" value="clades"/>
363 <has_size value="8999600" delta="300"/> 363 <has_size value="8999600" delta="300"/>
364 </assert_contents> 364 </assert_contents>
365 </output> 365 </output>
366 </test> 366 </test>
367 <test expect_num_outputs="5"> 367 <test expect_num_outputs="5">
368 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> 368 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
369 <conditional name="matutils_mode"> 369 <conditional name="matutils_mode">
370 <param name="options_mode" value="extract"/> 370 <param name="options_mode" value="extract"/>
371 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/> 371 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
372 <conditional name="operation_mode"> 372 <conditional name="operation_mode">
373 <param name="operation" value="max-epps"/> 373 <param name="operation" value="max-epps"/>
383 <has_size value="8999600" delta="300"/> 383 <has_size value="8999600" delta="300"/>
384 </assert_contents> 384 </assert_contents>
385 </output> 385 </output>
386 </test> 386 </test>
387 <test expect_num_outputs="5"> 387 <test expect_num_outputs="5">
388 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> 388 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
389 <conditional name="matutils_mode"> 389 <conditional name="matutils_mode">
390 <param name="options_mode" value="extract"/> 390 <param name="options_mode" value="extract"/>
391 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/> 391 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/>
392 <conditional name="operation_mode"> 392 <conditional name="operation_mode">
393 <param name="operation" value="max-parsimony"/> 393 <param name="operation" value="max-parsimony"/>
403 <has_size value="1183300" delta="300"/> 403 <has_size value="1183300" delta="300"/>
404 </assert_contents> 404 </assert_contents>
405 </output> 405 </output>
406 </test> 406 </test>
407 <test expect_num_outputs="3"> 407 <test expect_num_outputs="3">
408 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> 408 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
409 <conditional name="matutils_mode"> 409 <conditional name="matutils_mode">
410 <param name="options_mode" value="extract"/> 410 <param name="options_mode" value="extract"/>
411 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths"/> 411 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths"/>
412 <conditional name="operation_mode"> 412 <conditional name="operation_mode">
413 <param name="operation" value="max-branch-length"/> 413 <param name="operation" value="max-branch-length"/>
417 <output name="selected_samples" file="test_19_sample_names.txt" ftype="txt"/> 417 <output name="selected_samples" file="test_19_sample_names.txt" ftype="txt"/>
418 <output name="path_mutations" file="test_19_path_mutations.tabular" ftype="tabular"/> 418 <output name="path_mutations" file="test_19_path_mutations.tabular" ftype="tabular"/>
419 <output name="path_clades" file="test_19_path_clades.tabular" ftype="tabular"/> 419 <output name="path_clades" file="test_19_path_clades.tabular" ftype="tabular"/>
420 </test> 420 </test>
421 <test expect_num_outputs="1"> 421 <test expect_num_outputs="1">
422 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> 422 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
423 <conditional name="matutils_mode"> 423 <conditional name="matutils_mode">
424 <param name="options_mode" value="summary"/> 424 <param name="options_mode" value="summary"/>
425 <param name="summary_options" value="general"/> 425 <param name="summary_options" value="general"/>
426 </conditional> 426 </conditional>
427 <output name="general_stats" file="test_20_general_stats.txt" ftype="txt"/> 427 <output name="general_stats" file="test_20_general_stats.txt" ftype="txt"/>
428 </test> 428 </test>
429 <test expect_num_outputs="4"> 429 <test expect_num_outputs="4">
430 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> 430 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
431 <conditional name="matutils_mode"> 431 <conditional name="matutils_mode">
432 <param name="options_mode" value="summary"/> 432 <param name="options_mode" value="summary"/>
433 <param name="summary_options" value="samples,clades,mutations,aberrant"/> 433 <param name="summary_options" value="samples,clades,mutations,aberrant"/>
434 </conditional> 434 </conditional>
435 <output name="samples_stats" file="test_21_sample_stats.tabular" ftype="tabular"/> 435 <output name="samples_stats" file="test_21_sample_stats.tabular" ftype="tabular"/>
436 <output name="clades_stats" file="test_21_clades_stats.tabular" ftype="tabular"/> 436 <output name="clades_stats" file="test_21_clades_stats.tabular" ftype="tabular"/>
437 <output name="mutations_stats" file="test_21_mutations_stats.tabular" ftype="tabular"/> 437 <output name="mutations_stats" file="test_21_mutations_stats.tabular" ftype="tabular"/>
438 <output name="aberrant_stats" file="test_21_aberrant_stats.tabular" ftype="tabular"/> 438 <output name="aberrant_stats" file="test_21_aberrant_stats.tabular" ftype="tabular"/>
439 </test> 439 </test>
440 <test expect_num_outputs="1"> 440 <test expect_num_outputs="1">
441 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> 441 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
442 <conditional name="matutils_mode"> 442 <conditional name="matutils_mode">
443 <param name="options_mode" value="uncertainty"/> 443 <param name="options_mode" value="uncertainty"/>
444 <param name="samples" value="sample_names.txt"/> 444 <param name="samples" value="sample_names.txt"/>
445 <param name="uncertainty_options" value="get-parsimony"/> 445 <param name="uncertainty_options" value="get-parsimony"/>
446 </conditional> 446 </conditional>
447 <output name="total_parsimony_tree" file="test_22_total_parsimony_tree.txt" ftype="txt"/> 447 <output name="total_parsimony_tree" file="test_22_total_parsimony_tree.txt" ftype="txt"/>
448 </test> 448 </test>
449 <test expect_num_outputs="2"> 449 <test expect_num_outputs="2">
450 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> 450 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
451 <conditional name="matutils_mode"> 451 <conditional name="matutils_mode">
452 <param name="options_mode" value="uncertainty"/> 452 <param name="options_mode" value="uncertainty"/>
453 <param name="samples" value="sample_names.txt"/> 453 <param name="samples" value="sample_names.txt"/>
454 <param name="uncertainty_options" value="find-epps,find-neighborhood"/> 454 <param name="uncertainty_options" value="find-epps,find-neighborhood"/>
455 </conditional> 455 </conditional>
456 <output name="equally_parsimonious" file="test_23_equally_parsimoniou.tabular" ftype="tabular"/> 456 <output name="equally_parsimonious" file="test_23_equally_parsimoniou.tabular" ftype="tabular"/>
457 <output name="neighbourhood" file="test_23_neighbourhood.tabular" ftype="tabular"/> 457 <output name="neighbourhood" file="test_23_neighbourhood.tabular" ftype="tabular"/>
458 </test> 458 </test>
459 <test expect_num_outputs="1"> 459 <test expect_num_outputs="1">
460 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> 460 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
461 <conditional name="matutils_mode"> 461 <conditional name="matutils_mode">
462 <param name="options_mode" value="mask"/> 462 <param name="options_mode" value="mask"/>
463 <param name="restricted_samples" value="sample_names.txt"/> 463 <param name="restricted_samples" value="sample_names.txt"/>
464 <param name="simplify" value="true"/> 464 <param name="simplify" value="true"/>
465 </conditional> 465 </conditional>
466 <output name="output_mat" file="test_24_restricted.pb" ftype="protobuf3"/> 466 <output name="output_mat" file="test_24_restricted.pb" ftype="protobuf3"/>
467 </test> 467 </test>
468 <test expect_num_outputs="1"> 468 <test expect_num_outputs="1">
469 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> 469 <param name="mutation_annotation_file" value="mutation_annotation.pb" ftype="protobuf3"/>
470 <conditional name="matutils_mode"> 470 <conditional name="matutils_mode">
471 <param name="options_mode" value="mask"/> 471 <param name="options_mode" value="mask"/>
472 <param name="rename_samples" value="rename_samples.tabular"/> 472 <param name="rename_samples" value="rename_samples.tabular"/>
473 </conditional> 473 </conditional>
474 <output name="output_mat" file="test_25_renamed.pb" ftype="protobuf3"/> 474 <output name="output_mat" file="test_25_renamed.pb" ftype="protobuf3"/>