Mercurial > repos > iuc > amrfinderplus
comparison amrfinderplus.xml @ 7:7844dbe4f8e2 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
| author | iuc |
|---|---|
| date | Thu, 30 May 2024 13:07:03 +0000 |
| parents | 1920244e2895 |
| children |
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| 6:1920244e2895 | 7:7844dbe4f8e2 |
|---|---|
| 6 <import>macro.xml</import> | 6 <import>macro.xml</import> |
| 7 </macros> | 7 </macros> |
| 8 <expand macro="biotools"/> | 8 <expand macro="biotools"/> |
| 9 <expand macro="requirements"/> | 9 <expand macro="requirements"/> |
| 10 <expand macro="version_command"/> | 10 <expand macro="version_command"/> |
| 11 | |
| 12 <command detect_errors="aggressive"><![CDATA[ | 11 <command detect_errors="aggressive"><![CDATA[ |
| 13 amrfinder | 12 amrfinder |
| 14 #*====================================== | 13 #*====================================== |
| 15 CPU option | 14 CPU option |
| 16 ======================================*# | 15 ======================================*# |
| 81 ]]></command> | 80 ]]></command> |
| 82 <inputs> | 81 <inputs> |
| 83 <!-- DB and file INPUT --> | 82 <!-- DB and file INPUT --> |
| 84 <section name="input_option" title="Input/Output options" expanded="true"> | 83 <section name="input_option" title="Input/Output options" expanded="true"> |
| 85 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database"> | 84 <param name="amrfinder_db_select" type="select" label="The amrfinderplus database"> |
| 86 <options from_data_table="amrfinderplus_database"> | 85 <options from_data_table="amrfinderplus_versioned_database"> |
| 87 <validator message="No amrfinderplus database is available" type="no_options"/> | 86 <filter type="static_value" value="3.12" column="db_version"/> |
| 87 <validator message="No amrfinderplus database is available" type="no_options"/> | |
| 88 </options> | 88 </options> |
| 89 </param> | 89 </param> |
| 90 <conditional name="input_mode"> | 90 <conditional name="input_mode"> |
| 91 <param name="input_select" type="select" label="Choose input type" help="Choose the type of files (nucleotide and/or protein to be analyzed)"> | 91 <param name="input_select" type="select" label="Choose input type" help="Choose the type of files (nucleotide and/or protein to be analyzed)"> |
| 92 <option value="nucleotide">Nucleotide</option> | 92 <option value="nucleotide">Nucleotide</option> |
| 207 </data> | 207 </data> |
| 208 </outputs> | 208 </outputs> |
| 209 <tests> | 209 <tests> |
| 210 <test expect_num_outputs="2"> <!-- TEST_1 simple nucleotide input --> | 210 <test expect_num_outputs="2"> <!-- TEST_1 simple nucleotide input --> |
| 211 <section name="input_option"> | 211 <section name="input_option"> |
| 212 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> | 212 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> |
| 213 <conditional name="input_mode"> | 213 <conditional name="input_mode"> |
| 214 <param name="input_select" value="nucleotide"/> | 214 <param name="input_select" value="nucleotide"/> |
| 215 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/> | 215 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/> |
| 216 </conditional> | 216 </conditional> |
| 217 </section> | 217 </section> |
| 218 <output name="amrfinderplus_report" value="test_1/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> | 218 <output name="amrfinderplus_report" ftype="tabular"> |
| 219 <output name="nucleotide_output" value="test_1/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> | 219 <assert_contents> |
| 220 <has_n_columns n="22"/> | |
| 221 <has_n_lines n="8"/> | |
| 222 <has_text text="optrA"/> | |
| 223 <has_text text="WP_063854496"/> | |
| 224 <has_text text="WP_063843211"/> | |
| 225 </assert_contents> | |
| 226 </output> | |
| 227 <output name="nucleotide_output" ftype="fasta"> | |
| 228 <assert_contents> | |
| 229 <has_n_lines n="142"/> | |
| 230 <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/> | |
| 231 <has_text text="TTGTCCAAAGCC"/> | |
| 232 </assert_contents> | |
| 233 </output> | |
| 220 </test> | 234 </test> |
| 221 <test expect_num_outputs="3"> <!-- TEST_2 nucleotide input and full options --> | 235 <test expect_num_outputs="3"> <!-- TEST_2 nucleotide input and full options --> |
| 222 <section name="input_option"> | 236 <section name="input_option"> |
| 223 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> | 237 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> |
| 224 <conditional name="input_mode"> | 238 <conditional name="input_mode"> |
| 225 <param name="input_select" value="nucleotide"/> | 239 <param name="input_select" value="nucleotide"/> |
| 226 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/> | 240 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/> |
| 227 <param name="nucleotide_flank5_size" value="150"/> | 241 <param name="nucleotide_flank5_size" value="150"/> |
| 228 </conditional> | 242 </conditional> |
| 233 <param name="organism" value="Enterococcus_faecalis"/> | 247 <param name="organism" value="Enterococcus_faecalis"/> |
| 234 <param name="report_common" value="true"/> | 248 <param name="report_common" value="true"/> |
| 235 </conditional> | 249 </conditional> |
| 236 </section> | 250 </section> |
| 237 <section name="options"> | 251 <section name="options"> |
| 238 <param name="ident_min" value="1"/> | 252 <param name="ident_min" value="0.1"/> |
| 239 <param name="coverage_min" value="0.1"/> | 253 <param name="coverage_min" value="0.1"/> |
| 240 <param name="translation_table" value="11"/> | 254 <param name="translation_table" value="11"/> |
| 241 <param name="plus" value="true"/> | 255 <param name="plus" value="true"/> |
| 242 <param name="report_all_equal" value="true"/> | 256 <param name="report_all_equal" value="true"/> |
| 243 <param name="print_node" value="true"/> | 257 <param name="print_node" value="true"/> |
| 244 <param name="name" value="test_2"/> | 258 <param name="name" value="test_2"/> |
| 245 <param name="log" value="true"/> | 259 <param name="log" value="true"/> |
| 246 </section> | 260 </section> |
| 247 <output name="amrfinderplus_report" value="test_2/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> | 261 <output name="amrfinderplus_report" ftype="tabular"> |
| 248 <output name="nucleotide_output" value="test_2/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> | 262 <assert_contents> |
| 249 <output name="nucleotide_flank5_output" value="test_2/amrfinderplus_flanking_output.fasta" ftype="fasta" lines_diff="1"/> | 263 <has_n_columns n="24"/> |
| 264 <has_n_lines n="13"/> | |
| 265 <has_text text="optrA"/> | |
| 266 <has_text text="WP_063854496"/> | |
| 267 </assert_contents> | |
| 268 </output> | |
| 269 <output name="nucleotide_output" ftype="fasta"> | |
| 270 <assert_contents> | |
| 271 <has_n_lines n="267"/> | |
| 272 <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/> | |
| 273 <has_text text="TTGTCCAAAGCC"/> | |
| 274 </assert_contents> | |
| 275 </output> | |
| 276 <output name="nucleotide_flank5_output" ftype="fasta"> | |
| 277 <assert_contents> | |
| 278 <has_n_lines n="298"/> | |
| 279 <has_text text=">contig_2:54987-57395 strand:- mupB mupirocin-resistant isoleucine--tRNA ligase MupB"/> | |
| 280 <has_text text="TTGTCCAAAGCC"/> | |
| 281 </assert_contents> | |
| 282 </output> | |
| 250 </test> | 283 </test> |
| 251 <test expect_num_outputs="2"> <!-- TEST_3 nucleotide input and several options --> | 284 <test expect_num_outputs="2"> <!-- TEST_3 nucleotide input and several options --> |
| 252 <section name="input_option"> | 285 <section name="input_option"> |
| 253 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> | 286 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> |
| 254 <conditional name="input_mode"> | 287 <conditional name="input_mode"> |
| 255 <param name="input_select" value="nucleotide"/> | 288 <param name="input_select" value="nucleotide"/> |
| 256 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/> | 289 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/> |
| 257 </conditional> | 290 </conditional> |
| 258 </section> | 291 </section> |
| 264 </conditional> | 297 </conditional> |
| 265 </section> | 298 </section> |
| 266 <section name="options"> | 299 <section name="options"> |
| 267 <param name="report_all_equal" value="true"/> | 300 <param name="report_all_equal" value="true"/> |
| 268 </section> | 301 </section> |
| 269 <output name="amrfinderplus_report" value="test_3/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> | 302 <output name="amrfinderplus_report" ftype="tabular"> |
| 270 <output name="nucleotide_output" value="test_3/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> | 303 <assert_contents> |
| 304 <has_n_columns n="22"/> | |
| 305 <has_n_lines n="9"/> | |
| 306 <has_text text="optrA"/> | |
| 307 <has_text text="WP_063854496"/> | |
| 308 <has_text text="WP_063856080"/> | |
| 309 </assert_contents> | |
| 310 </output> | |
| 311 <output name="nucleotide_output" ftype="fasta"> | |
| 312 <assert_contents> | |
| 313 <has_n_lines n="142"/> | |
| 314 <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/> | |
| 315 <has_text text="TTGTCCAAAGCC"/> | |
| 316 </assert_contents> | |
| 317 </output> | |
| 271 </test> | 318 </test> |
| 272 <test expect_num_outputs="2"> <!-- TEST_4 simple protein input --> | 319 <test expect_num_outputs="2"> <!-- TEST_4 simple protein input --> |
| 273 <section name="input_option"> | 320 <section name="input_option"> |
| 274 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> | 321 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> |
| 275 <conditional name="input_mode"> | 322 <conditional name="input_mode"> |
| 276 <param name="input_select" value="protein"/> | 323 <param name="input_select" value="protein"/> |
| 277 <param name="protein_input" value="enterococcus_faecalis.faa"/> | 324 <param name="protein_input" value="enterococcus_faecalis.faa"/> |
| 278 </conditional> | 325 </conditional> |
| 279 </section> | 326 </section> |
| 280 <output name="amrfinderplus_report" value="test_4/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> | 327 <output name="amrfinderplus_report" ftype="tabular"> |
| 281 <output name="protein_output" value="test_4/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/> | 328 <assert_contents> |
| 329 <has_n_columns n="18"/> | |
| 330 <has_n_lines n="7"/> | |
| 331 <has_text text="optrA"/> | |
| 332 <has_text text="WP_063854496"/> | |
| 333 <has_text text="WP_063856080"/> | |
| 334 </assert_contents> | |
| 335 </output> | |
| 336 <output name="protein_output" ftype="fasta"> | |
| 337 <assert_contents> | |
| 338 <has_n_lines n="49"/> | |
| 339 <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/> | |
| 340 <has_text text="SDYIVLTEIQKSIDDVKRCQGNYF"/> | |
| 341 </assert_contents> | |
| 342 </output> | |
| 282 </test> | 343 </test> |
| 283 <test expect_num_outputs="2"> <!-- TEST_5 protein input and full options to gff3 and bakta --> | 344 <test expect_num_outputs="2"> <!-- TEST_5 protein input and full options to gff3 and bakta --> |
| 284 <section name="input_option"> | 345 <section name="input_option"> |
| 285 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> | 346 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> |
| 286 <conditional name="input_mode"> | 347 <conditional name="input_mode"> |
| 287 <param name="input_select" value="protein"/> | 348 <param name="input_select" value="protein"/> |
| 288 <param name="protein_input" value="enterococcus_faecalis.faa"/> | 349 <param name="protein_input" value="enterococcus_faecalis.faa"/> |
| 289 <param name="gff_annotation" value="enterococcus_faecalis_bakta.gff3"/> | 350 <param name="gff_annotation" value="enterococcus_faecalis_bakta.gff3"/> |
| 290 <param name="annotation_format" value="bakta"/> | 351 <param name="annotation_format" value="bakta"/> |
| 304 <param name="plus" value="true"/> | 365 <param name="plus" value="true"/> |
| 305 <param name="report_all_equal" value="true"/> | 366 <param name="report_all_equal" value="true"/> |
| 306 <param name="print_node" value="true"/> | 367 <param name="print_node" value="true"/> |
| 307 <param name="name" value="test_5"/> | 368 <param name="name" value="test_5"/> |
| 308 </section> | 369 </section> |
| 309 <output name="amrfinderplus_report" value="test_5/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> | 370 <output name="amrfinderplus_report" ftype="tabular"> |
| 310 <output name="protein_output" value="test_5/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> | 371 <assert_contents> |
| 372 <has_n_columns n="24"/> | |
| 373 <has_n_lines n="8"/> | |
| 374 <has_text text="optrA"/> | |
| 375 <has_text text="IDOBJL_14770"/> | |
| 376 <has_text text="WP_063856080"/> | |
| 377 </assert_contents> | |
| 378 </output> | |
| 379 <output name="nucleotide_output" ftype="fasta"> | |
| 380 <assert_contents> | |
| 381 <has_n_lines n="49"/> | |
| 382 <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/> | |
| 383 <has_text text="SDYIVLTEIQKSIDDVKRCQGNYF"/> | |
| 384 </assert_contents> | |
| 385 </output> | |
| 311 </test> | 386 </test> |
| 312 <test expect_num_outputs="2"> <!-- TEST_6 protein input and prokka annotation --> | 387 <test expect_num_outputs="2"> <!-- TEST_6 protein input and prokka annotation --> |
| 313 <section name="input_option"> | 388 <section name="input_option"> |
| 314 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> | 389 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> |
| 315 <conditional name="input_mode"> | 390 <conditional name="input_mode"> |
| 316 <param name="input_select" value="protein"/> | 391 <param name="input_select" value="protein"/> |
| 317 <param name="protein_input" value="PROKKA_05252023.faa"/> | 392 <param name="protein_input" value="PROKKA_05252023.faa"/> |
| 318 <param name="gff_annotation" value="PROKKA_05252023.gff"/> | 393 <param name="gff_annotation" value="PROKKA_05252023.gff"/> |
| 319 <param name="annotation_format" value="prokka"/> | 394 <param name="annotation_format" value="prokka"/> |
| 320 </conditional> | 395 </conditional> |
| 321 </section> | 396 </section> |
| 322 <output name="amrfinderplus_report" value="test_6/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> | 397 <output name="amrfinderplus_report" ftype="tabular"> |
| 323 <output name="protein_output" value="test_6/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/> | 398 <assert_contents> |
| 399 <has_n_columns n="22"/> | |
| 400 <has_n_lines n="7"/> | |
| 401 <has_text text="FODBOAIN_02586"/> | |
| 402 <has_text text="WP_063856395"/> | |
| 403 </assert_contents> | |
| 404 </output> | |
| 405 <output name="protein_output" ftype="fasta"> | |
| 406 <assert_contents> | |
| 407 <has_n_lines n="49"/> | |
| 408 <has_text text=">FODBOAIN_02586 optrA ABC-F type ribosomal protection protein OptrA"/> | |
| 409 <has_text text="YSNLLLLFSGIIVISWLVTLNVYKHSQRDF"/> | |
| 410 </assert_contents> | |
| 411 </output> | |
| 324 </test> | 412 </test> |
| 325 <test expect_num_outputs="2"> <!-- TEST_7 protein input and genbank default annotation --> | 413 <test expect_num_outputs="2"> <!-- TEST_7 protein input and genbank default annotation --> |
| 326 <section name="input_option"> | 414 <section name="input_option"> |
| 327 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> | 415 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> |
| 328 <conditional name="input_mode"> | 416 <conditional name="input_mode"> |
| 329 <param name="input_select" value="protein"/> | 417 <param name="input_select" value="protein"/> |
| 330 <param name="protein_input" value="input_ncbi.faa"/> | 418 <param name="protein_input" value="input_ncbi.faa"/> |
| 331 <param name="gff_annotation" value="annotation_ncbi.gff3"/> | 419 <param name="gff_annotation" value="annotation_ncbi.gff3"/> |
| 332 </conditional> | 420 </conditional> |
| 333 </section> | 421 </section> |
| 334 <output name="amrfinderplus_report" value="test_7/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> | 422 <output name="amrfinderplus_report" ftype="tabular"> |
| 335 <output name="protein_output" value="test_7/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/> | 423 <assert_contents> |
| 424 <has_n_columns n="22"/> | |
| 425 <has_n_lines n="4"/> | |
| 426 <has_text text="blaOXA"/> | |
| 427 <has_text text="WP_063855540"/> | |
| 428 </assert_contents> | |
| 429 </output> | |
| 430 <output name="protein_output" ftype="fasta"> | |
| 431 <assert_contents> | |
| 432 <has_n_lines n="17"/> | |
| 433 <has_text text=">blaOXA-436_partial blaOXA OXA-48 family class D beta-lactamase"/> | |
| 434 <has_text text="SSNPDAAPVSS"/> | |
| 435 </assert_contents> | |
| 436 </output> | |
| 336 </test> | 437 </test> |
| 337 <test expect_num_outputs="3"> <!-- TEST_8 both protein and nucleotide input --> | 438 <test expect_num_outputs="3"> <!-- TEST_8 both protein and nucleotide input --> |
| 338 <section name="input_option"> | 439 <section name="input_option"> |
| 339 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> | 440 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> |
| 340 <conditional name="input_mode"> | 441 <conditional name="input_mode"> |
| 341 <param name="input_select" value="nucl_prot"/> | 442 <param name="input_select" value="nucl_prot"/> |
| 342 <param name="protein_input" value="enterococcus_faecalis.faa"/> | 443 <param name="protein_input" value="enterococcus_faecalis.faa"/> |
| 343 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/> | 444 <param name="nucleotide_input" value="enterococcus_faecalis.fna"/> |
| 344 <param name="gff_annotation" value="enterococcus_faecalis_bakta.gff3"/> | 445 <param name="gff_annotation" value="enterococcus_faecalis_bakta.gff3"/> |
| 349 <conditional name="organism_conditionnal"> | 450 <conditional name="organism_conditionnal"> |
| 350 <param name="organism_select" value="add_organism"/> | 451 <param name="organism_select" value="add_organism"/> |
| 351 <param name="organism" value="Enterococcus_faecalis"/> | 452 <param name="organism" value="Enterococcus_faecalis"/> |
| 352 </conditional> | 453 </conditional> |
| 353 </section> | 454 </section> |
| 354 <output name="amrfinderplus_report" value="test_8/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> | 455 <output name="amrfinderplus_report" ftype="tabular"> |
| 355 <output name="protein_output" value="test_8/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/> | 456 <assert_contents> |
| 356 <output name="nucleotide_output" value="test_8/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> | 457 <has_n_columns n="22"/> |
| 458 <has_n_lines n="8"/> | |
| 459 <has_text text="IDOBJL_14770"/> | |
| 460 <has_text text="WP_063856080"/> | |
| 461 </assert_contents> | |
| 462 </output> | |
| 463 <output name="nucleotide_output" ftype="fasta"> | |
| 464 <assert_contents> | |
| 465 <has_n_lines n="143"/> | |
| 466 <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/> | |
| 467 <has_text text="CTTATCTGTATAG"/> | |
| 468 </assert_contents> | |
| 469 </output> | |
| 470 <output name="protein_output" ftype="fasta"> | |
| 471 <assert_contents> | |
| 472 <has_n_lines n="37"/> | |
| 473 <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/> | |
| 474 <has_text text="QEAGAGMSLLNFT"/> | |
| 475 </assert_contents> | |
| 476 </output> | |
| 357 </test> | 477 </test> |
| 358 <test expect_num_outputs="4"> <!-- TEST_9 rast annotation and mutation all results --> | 478 <test expect_num_outputs="4"> <!-- TEST_9 rast annotation and mutation all results --> |
| 359 <section name="input_option"> | 479 <section name="input_option"> |
| 360 <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/> | 480 <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/> |
| 361 <conditional name="input_mode"> | 481 <conditional name="input_mode"> |
| 362 <param name="input_select" value="nucl_prot"/> | 482 <param name="input_select" value="nucl_prot"/> |
| 363 <param name="protein_input" value="e_faecalis_rast.faa"/> | 483 <param name="protein_input" value="e_faecalis_rast.faa"/> |
| 364 <param name="nucleotide_input" value="e_faecalis_rast.fna"/> | 484 <param name="nucleotide_input" value="e_faecalis_rast.fna"/> |
| 365 <param name="gff_annotation" value="e_faecalis_rast.gff"/> | 485 <param name="gff_annotation" value="e_faecalis_rast.gff"/> |
| 378 <param name="coverage_min" value="0.1"/> | 498 <param name="coverage_min" value="0.1"/> |
| 379 <param name="plus" value="true"/> | 499 <param name="plus" value="true"/> |
| 380 <param name="print_node" value="true"/> | 500 <param name="print_node" value="true"/> |
| 381 <param name="name" value="test_5"/> | 501 <param name="name" value="test_5"/> |
| 382 </section> | 502 </section> |
| 383 <output name="amrfinderplus_report" value="test_9/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/> | 503 <output name="amrfinderplus_report" ftype="tabular"> |
| 384 <output name="protein_output" value="test_9/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/> | 504 <assert_contents> |
| 385 <output name="nucleotide_output" value="test_9/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/> | 505 <has_n_columns n="24"/> |
| 386 <output name="mutation_all_report" value="test_9/amrfinderplus_mutation_all.tsv" ftype="tabular" lines_diff="1"/> | 506 <has_n_lines n="2"/> |
| 507 <has_text text="MUPIROCIN"/> | |
| 508 <has_text text="WP_063854488"/> | |
| 509 </assert_contents> | |
| 510 </output> | |
| 511 <output name="nucleotide_output" ftype="fasta"> | |
| 512 <assert_contents> | |
| 513 <has_n_lines n="40"/> | |
| 514 <has_text text=">contig00019:27227-29524 strand:+ mupB mupirocin-resistant isoleucine--tRNA ligase MupB"/> | |
| 515 <has_text text="ATCAGTCGTGAAATAGAA"/> | |
| 516 </assert_contents> | |
| 517 </output> | |
| 518 <output name="protein_output" ftype="fasta"> | |
| 519 <assert_contents> | |
| 520 <has_n_lines n="0"/> | |
| 521 </assert_contents> | |
| 522 </output> | |
| 523 <output name="mutation_all_report" ftype="tabular"> | |
| 524 <assert_contents> | |
| 525 <has_n_columns n="24"/> | |
| 526 <has_n_lines n="5"/> | |
| 527 <has_text text="23S_GA375AG"/> | |
| 528 <has_text text="NZ_CP04"/> | |
| 529 </assert_contents> | |
| 530 </output> | |
| 387 </test> | 531 </test> |
| 388 </tests> | 532 </tests> |
| 389 <help><![CDATA[ | 533 <help><![CDATA[ |
| 390 **What it does** | 534 **What it does** |
| 391 | 535 |