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comparison datasets_genome.xml @ 15:198c75abbf55 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
author iuc
date Mon, 04 Mar 2024 17:27:59 +0000
parents 75acf92c8fd5
children a6a475ed58cb
comparison
equal deleted inserted replaced
14:75acf92c8fd5 15:198c75abbf55
31 #end if 31 #end if
32 #if $filters.chromosomes: 32 #if $filters.chromosomes:
33 --chromosomes '$filters.chromosomes' 33 --chromosomes '$filters.chromosomes'
34 #end if 34 #end if
35 $filters.exclude_atypical 35 $filters.exclude_atypical
36 #if $filters.mag:
37 --mag '$filters.mag'
38 #end if
39
36 @INCLUDE@ 40 @INCLUDE@
37 @RELEASED_BEFORE@ 41 @RELEASED_BEFORE@
38 @RELEASED_AFTER@ 42 @RELEASED_AFTER@
39 #for search_term in $filters.search: 43 #for search_term in $filters.search:
40 --search '$filters.search_term' 44 --search '$filters.search_term'
104 <option value="all">All</option> 108 <option value="all">All</option>
105 </param> 109 </param>
106 <expand macro="assembly_source"/> 110 <expand macro="assembly_source"/>
107 <expand macro="chromosomes"/> 111 <expand macro="chromosomes"/>
108 <param argument="--exclude-atypical" type="boolean" truevalue="--exclude-atypical" falsevalue="" label="Exclude atypical assemblies"/> 112 <param argument="--exclude-atypical" type="boolean" truevalue="--exclude-atypical" falsevalue="" label="Exclude atypical assemblies"/>
113 <param argument="--mag" type="select" multiple="false" optional="true" label="Filter metagenome assembled genomes (MAGs)">
114 <option value="only" selected="false">Limit to MAGs</option>
115 <option value="exclude" selected="false">Exclude MAGs</option>
116 </param>
109 <expand macro="released_options"/> 117 <expand macro="released_options"/>
110 <expand macro="released_options" before_or_after="after"/> 118 <expand macro="released_options" before_or_after="after"/>
111 119
112 <repeat name="search" title="Add search terms"> 120 <repeat name="search" title="Add search terms">
113 <param argument="--search" type="text" label="Only include genomes that have the specified text in the searchable fields" help="Searchable fields are species and infraspecies, assembly name and submitter"/> 121 <param argument="--search" type="text" label="Only include genomes that have the specified text in the searchable fields" help="Searchable fields are species and infraspecies, assembly name and submitter"/>
330 <param name="include" value="seq-report,gff3,gbff"/> 338 <param name="include" value="seq-report,gff3,gbff"/>
331 <param name="decompress" value="true"/> 339 <param name="decompress" value="true"/>
332 </section> 340 </section>
333 <output name="genome_data_report"> 341 <output name="genome_data_report">
334 <assert_contents> 342 <assert_contents>
335 <has_text text="GCF_000013305.1"/> 343 <has_text text="GCF_000013305.1"/>
336 <has_text text="GCF_000007445.1"/> 344 <has_text text="GCF_000007445.1"/>
337 <has_n_lines n="3"/> 345 <has_n_lines n="3"/>
338 <has_n_columns n="4"/> 346 <has_n_columns n="4"/>
339 </assert_contents> 347 </assert_contents>
340 </output> 348 </output>
341 <output_collection name="genomic_gff" type="list"> 349 <output_collection name="genomic_gff" type="list">
347 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gbff" compare="contains"/> 355 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gbff" compare="contains"/>
348 </output_collection> 356 </output_collection>
349 </test> 357 </test>
350 358
351 <!-- should not fail https://github.com/ncbi/datasets/issues/194 --> 359 <!-- should not fail https://github.com/ncbi/datasets/issues/194 -->
352 <test expect_num_outputs="2"> <!-- expect_failure="true"> --> 360 <test expect_num_outputs="2">
353 <conditional name="query|subcommand"> 361 <conditional name="query|subcommand">
354 <param name="download_by" value="accession"/> 362 <param name="download_by" value="accession"/>
355 <conditional name="text_or_file"> 363 <conditional name="text_or_file">
356 <param name="text_or_file" value="text"/> 364 <param name="text_or_file" value="text"/>
357 <param name="accession" value="GCF_000001405"/> 365 <param name="accession" value="GCF_000001405"/>
360 <param name="released_before" value="01/01/2015"/> 368 <param name="released_before" value="01/01/2015"/>
361 <param name="assembly_version" value="all"/> 369 <param name="assembly_version" value="all"/>
362 <section name="file_choices"> 370 <section name="file_choices">
363 <param name="include" value="seq-report"/> 371 <param name="include" value="seq-report"/>
364 </section> 372 </section>
365 <!-- 373 <output name="genome_data_report">
366 <output_collection name="sequence_report" type="list" count="4" > 374 <!-- assert that we get at least the 16 versions available at the time of writing this test -->
367 --> 375 <assert_contents>
376 <has_text text="GCF_000001405" min="16"/>
377 <has_n_lines min="16"/>
378 <has_n_columns n="4"/>
379 </assert_contents>
380 </output>
381 <!--not testing the collection output. the count will change over time
382 and this can't be tested for at the moment
383 <output_collection name="sequence_report" type="list" count="16"/> -->
368 </test> 384 </test>
369 <test expect_num_outputs="5"> 385 <test expect_num_outputs="5">
370 <conditional name="query|subcommand"> 386 <conditional name="query|subcommand">
371 <param name="download_by" value="accession"/> 387 <param name="download_by" value="accession"/>
372 <conditional name="text_or_file"> 388 <conditional name="text_or_file">
411 </section> 427 </section>
412 <output_collection name="genome_fasta" type="list:list" count="1"> 428 <output_collection name="genome_fasta" type="list:list" count="1">
413 <element name="GCF_000146045.2"> 429 <element name="GCF_000146045.2">
414 <element name="GCF_000146045.2_R64" ftype="fasta.gz"> 430 <element name="GCF_000146045.2_R64" ftype="fasta.gz">
415 <assert_contents> 431 <assert_contents>
416 <has_size value="3843460"/> 432 <has_size value="3843460" delta="2000"/>
417 </assert_contents> 433 </assert_contents>
418 </element> 434 </element>
419 </element> 435 </element>
420 </output_collection> 436 </output_collection>
421 <output_collection name="protein_fasta" type="list" count="1"> 437 <output_collection name="protein_fasta" type="list" count="1">
422 <element name="GCF_000146045.2" ftype="fasta.gz"> 438 <element name="GCF_000146045.2" ftype="fasta.gz">
423 <assert_contents> 439 <assert_contents>
424 <has_size value="1845038"/> 440 <has_size value="1845038" delta="2000"/>
425 </assert_contents> 441 </assert_contents>
426 </element> 442 </element>
427 </output_collection> 443 </output_collection>
428 <output_collection name="rna_fasta" type="list" count="1"> 444 <output_collection name="rna_fasta" type="list" count="1">
429 <element name="GCF_000146045.2" ftype="fasta.gz"> 445 <element name="GCF_000146045.2" ftype="fasta.gz">
430 <assert_contents> 446 <assert_contents>
431 <has_size value="2784899"/> 447 <has_size value="2784899" delta="2000"/>
432 </assert_contents> 448 </assert_contents>
433 </element> 449 </element>
434 </output_collection> 450 </output_collection>
435 </test> 451 </test>
436 <test expect_num_outputs="3"> 452 <test expect_num_outputs="3">
449 <output_collection name="genome_fasta" type="list:list" count="2"> 465 <output_collection name="genome_fasta" type="list:list" count="2">
450 <expand macro="genome_fasta_assert" el1="GCF_000002945.1" el2="GCF_000002945.1_ASM294v2" expression=">NC_[0-9]+\.[0-9]+ Schizosaccharomyces pombe (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="4"/> 466 <expand macro="genome_fasta_assert" el1="GCF_000002945.1" el2="GCF_000002945.1_ASM294v2" expression=">NC_[0-9]+\.[0-9]+ Schizosaccharomyces pombe (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="4"/>
451 <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression=">NC_[0-9]+\.[0-9]+ Saccharomyces cerevisiae S288[Cc] (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="17"/> 467 <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression=">NC_[0-9]+\.[0-9]+ Saccharomyces cerevisiae S288[Cc] (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="17"/>
452 </output_collection> 468 </output_collection>
453 </test> 469 </test>
454 <!-- tax_exact_match seems not able to filter out strains 470 <!-- tax_exact_match should filter out strains
455 https://github.com/ncbi/datasets/issues/187 471 https://github.com/ncbi/datasets/issues/187 -->
456 hence we set expect_test_failure="true"--> 472 <test expect_num_outputs="1">
457 <test expect_num_outputs="1" expect_test_failure="true">
458 <conditional name="query|subcommand"> 473 <conditional name="query|subcommand">
459 <param name="download_by" value="taxon"/> 474 <param name="download_by" value="taxon"/>
460 <param name="taxon_positional" value="4932"/> 475 <param name="taxon_positional" value="4932"/>
461 <param name="tax_exact_match" value="true"/> 476 <param name="tax_exact_match" value="true"/>
462 </conditional> 477 </conditional>