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comparison staramr_search.xml @ 17:141afacabcfa draft

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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303
author nml
date Thu, 31 Aug 2023 15:55:49 +0000
parents 4d83eccf5f81
children 3b22de20bd4b
comparison
equal deleted inserted replaced
16:4d83eccf5f81 17:141afacabcfa
1 <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0" profile="16.04"> 1 <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0" profile="16.04">
2 <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description> 2 <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">0.9.1</token> 4 <token name="@VERSION@">0.10.0</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@VERSION@">staramr</requirement> 7 <requirement type="package" version="@VERSION@">staramr</requirement>
8 <!-- The staramr conda package includes the mlst software, but the list of schemes 8 <!-- The staramr conda package includes the mlst software, but the list of schemes
9 changes depending on the version. I specify the exact version here to make sure 9 changes depending on the version. I specify the exact version here to make sure
50 #if str($advanced.exclude_genes.exclude_genes_condition) == 'custom' 50 #if str($advanced.exclude_genes.exclude_genes_condition) == 'custom'
51 --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}' 51 --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}'
52 #elif str($advanced.exclude_genes.exclude_genes_condition) == 'none' 52 #elif str($advanced.exclude_genes.exclude_genes_condition) == 'none'
53 --no-exclude-genes 53 --no-exclude-genes
54 #end if 54 #end if
55
56
57 #if str($advanced.complex_mutations.complex_mutations_condition) == 'custom'
58 --complex-mutations-file '${advanced.complex_mutations.complex_mutations_file}'
59 #end if
55 60
56 #if str($advanced.plasmidfinder_type) != 'include_all' 61 #if str($advanced.plasmidfinder_type) != 'include_all'
57 --plasmidfinder-database-type '${advanced.plasmidfinder_type}' 62 --plasmidfinder-database-type '${advanced.plasmidfinder_type}'
58 #end if 63 #end if
59 64
290 <when value="default" /> 295 <when value="default" />
291 <when value="custom"> 296 <when value="custom">
292 <param type="data" name="exclude_genes_file" format="txt,tabular" label="Exclude genes file" help="Pass a file containing a list of genes to exclude from the ResFinder/PointFinder results" /> 297 <param type="data" name="exclude_genes_file" format="txt,tabular" label="Exclude genes file" help="Pass a file containing a list of genes to exclude from the ResFinder/PointFinder results" />
293 </when> 298 </when>
294 <when value="none" /> 299 <when value="none" />
300 </conditional>
301 <conditional name="complex_mutations">
302 <param name="complex_mutations_condition" type="select" label="Provide a custom list of complex mutations">
303 <option value="default" selected="true">Use default list of complex mutations</option>
304 <option value="custom">Provide a custom list of complex mutations</option>
305 </param>
306 <when value="default" />
307 <when value="custom">
308 <param type="data" name="complex_mutations_file" format="txt,tabular" label="Complex mutations file" help="Pass a file containing a list of complex mutations to group (if present) in the PointFinder results" />
309 </when>
295 </conditional> 310 </conditional>
296 <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type"> 311 <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type">
297 <option value="include_all" selected="true">Include all available database types</option> 312 <option value="include_all" selected="true">Include all available database types</option>
298 <option value="gram_positive">Gram Positive</option> 313 <option value="gram_positive">Gram Positive</option>
299 <option value="enterobacteriaceae">Enterobacteriaceae</option> 314 <option value="enterobacteriaceae">Enterobacteriaceae</option>
314 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits"> 329 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits">
315 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" /> 330 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" />
316 </collection> 331 </collection>
317 </outputs> 332 </outputs>
318 <tests> 333 <tests>
319 <test> 334 <test expect_num_outputs="9">
320 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> 335 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
321 <param name="use_pointfinder" value="salmonella" /> 336 <param name="use_pointfinder" value="salmonella" />
322 337
323 <output name="summary" file="test1-summary.tsv" ftype="tabular" /> 338 <output name="summary" file="test1-summary.tsv" ftype="tabular" />
324 <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" /> 339 <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" />
325 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" /> 340 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
326 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> 341 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
327 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" /> 342 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" />
328 <output_collection name="blast_hits" type="list"> 343 <output_collection name="blast_hits" type="list">
329 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> 344 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
330 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> 345 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
331 </output_collection> 346 </output_collection>
332 </test> 347 </test>
333 <test> 348 <test expect_num_outputs="9">
334 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> 349 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
335 <param name="use_pointfinder" value="escherichia_coli" /> 350 <param name="use_pointfinder" value="escherichia_coli" />
336 351
337 <output name="summary" file="test1-summary-ecoli.tsv" ftype="tabular" /> 352 <output name="summary" file="test1-summary-ecoli.tsv" ftype="tabular" />
338 <output name="detailed_summary" file="test1-detailed-summary-ecoli.tsv" ftype="tabular" /> 353 <output name="detailed_summary" file="test1-detailed-summary-ecoli.tsv" ftype="tabular" />
339 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" /> 354 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
340 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> 355 <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
341 <output name="pointfinder" file="test1-pointfinder-ecoli.tsv" ftype="tabular" /> 356 <output name="pointfinder" file="test1-pointfinder-ecoli.tsv" ftype="tabular" />
342 </test> 357 </test>
343 <test> 358 <test expect_num_outputs="8">
344 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> 359 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
345 360
346 <output name="summary" file="test2-summary.tsv" ftype="tabular" /> 361 <output name="summary" file="test2-summary.tsv" ftype="tabular" />
347 <output name="resfinder" file="test2-resfinder.tsv" ftype="tabular" /> 362 <output name="resfinder" file="test2-resfinder.tsv" ftype="tabular" />
348 <output_collection name="blast_hits" type="list"> 363 <output_collection name="blast_hits" type="list">
349 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> 364 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
350 </output_collection> 365 </output_collection>
351 </test> 366 </test>
352 <test> 367 <test expect_num_outputs="8">
353 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> 368 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
354 <section name="advanced"> 369 <section name="advanced">
355 <param name="mlst_scheme" value="listeria_2" /> 370 <param name="mlst_scheme" value="listeria_2" />
356 </section> 371 </section>
357 <output name="mlst" file="mlst.tsv" ftype="tabular" /> 372 <output name="mlst" file="mlst.tsv" ftype="tabular" />
358 </test> 373 </test>
359 <test> 374 <test expect_num_outputs="8">
360 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" /> 375 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
361 <param name="pid_threshold" value="99.8" /> 376 <param name="pid_threshold" value="99.8" />
362 377
363 <output name="summary" file="test3-summary.tsv" ftype="tabular" /> 378 <output name="summary" file="test3-summary.tsv" ftype="tabular" />
364 </test> 379 </test>
365 <test> 380 <test expect_num_outputs="8">
366 <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" ftype="fasta" /> 381 <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" ftype="fasta" />
367 <param name="pid_threshold" value="99.8" /> 382 <param name="pid_threshold" value="99.8" />
368 383
369 <output name="summary" file="test4-summary.tsv" ftype="tabular" /> 384 <output name="summary" file="test4-summary.tsv" ftype="tabular" />
370 </test> 385 </test>
371 <test> 386 <test expect_num_outputs="8">
372 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> 387 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
373 388
374 <output name="summary" file="test5-summary.tsv" ftype="tabular" /> 389 <output name="summary" file="test5-summary.tsv" ftype="tabular" />
375 </test> 390 </test>
376 <test> 391 <test expect_num_outputs="8">
377 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> 392 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
378 <param name="exclude_genes_condition" value="none" /> 393 <param name="exclude_genes_condition" value="none" />
379 394
380 <output name="summary" file="test6-summary.tsv" ftype="tabular" /> 395 <output name="summary" file="test6-summary.tsv" ftype="tabular" />
381 </test> 396 </test>
382 <test> 397 <test expect_num_outputs="8">
383 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> 398 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
384 <param name="exclude_genes_condition" value="custom" /> 399 <param name="exclude_genes_condition" value="custom" />
385 <param name="exclude_genes_file" value="genes_to_exclude.tsv" /> 400 <param name="exclude_genes_file" value="genes_to_exclude.tsv" />
386 401
387 <output name="summary" file="test5-summary.tsv" ftype="tabular" /> 402 <output name="summary" file="test5-summary.tsv" ftype="tabular" />
388 </test> 403 </test>
389 <test> 404 <test expect_num_outputs="8">
390 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" /> 405 <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
391 <param name="genome_size_lower_bound" value="1" /> 406 <param name="genome_size_lower_bound" value="1" />
392 <param name="genome_size_upper_bound" value="10" /> 407 <param name="genome_size_upper_bound" value="10" />
393 408
394 <output name="summary" file="test8-summary.tsv" ftype="tabular"/> 409 <output name="summary" file="test8-summary.tsv" ftype="tabular"/>