Mercurial > repos > iuc > semibin
comparison semibin.xml @ 1:6b517dc161e4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
| author | iuc |
|---|---|
| date | Mon, 27 Mar 2023 08:25:14 +0000 |
| parents | 7b382efabb98 |
| children | 99ff9221182c |
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| 0:7b382efabb98 | 1:6b517dc161e4 |
|---|---|
| 108 </collection> | 108 </collection> |
| 109 <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering"> | 109 <collection name="output_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering"> |
| 110 <filter>mode["select"]!="multi"</filter> | 110 <filter>mode["select"]!="multi"</filter> |
| 111 <discover_datasets pattern=".*?\.(?P<designation>.*).fa" format="fasta" directory="output/output_bins" /> | 111 <discover_datasets pattern=".*?\.(?P<designation>.*).fa" format="fasta" directory="output/output_bins" /> |
| 112 </collection> | 112 </collection> |
| 113 <collection name="multi_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering"> | 113 <collection name="multi_bins" type="list" label="${tool.name} on ${on_string}: Reconstructed bins before reclustering (multi_bins)"> |
| 114 <filter>mode["select"]=="multi"</filter> | 114 <filter>mode["select"]=="multi"</filter> |
| 115 <discover_datasets pattern=".*?\.(?P<designation>.*).fa" format="fasta" directory="output/bins" /> | 115 <discover_datasets pattern=".*?\.(?P<designation>.*).fa" format="fasta" directory="output/bins" /> |
| 116 </collection> | 116 </collection> |
| 117 <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data"> | 117 <data name="single_data" format="csv" from_work_dir="output/data.csv" label="${tool.name} on ${on_string}: Training data"> |
| 118 <filter>(mode["select"]=="single" or mode["select"]=="co") and extra_output and "data" in extra_output</filter> | 118 <filter>(mode["select"]=="single" or mode["select"]=="co") and extra_output and "data" in extra_output</filter> |
| 156 <param name="batch_size" value="2048"/> | 156 <param name="batch_size" value="2048"/> |
| 157 </section> | 157 </section> |
| 158 <section name="bin"> | 158 <section name="bin"> |
| 159 <param name="max_node" value="1"/> | 159 <param name="max_node" value="1"/> |
| 160 <param name="max_edges" value="200"/> | 160 <param name="max_edges" value="200"/> |
| 161 <param name="minfasta_kbs" value="200"/> | 161 <param name="minfasta_kbs" value="2"/> |
| 162 <param name="no_recluster" value="false"/> | 162 <param name="no_recluster" value="false"/> |
| 163 </section> | 163 </section> |
| 164 <param name="extra_output" value="data,coverage,contigs"/> | 164 <param name="extra_output" value="data,coverage,contigs"/> |
| 165 <output_collection name="output_recluster_bins" count="0"/> | 165 <output_collection name="output_recluster_bins" count="39"> |
| 166 <output_collection name="output_bins" count="3"> | 166 <element name="0" ftype="fasta"> |
| 167 <element name="0" ftype="fasta"> | |
| 168 <assert_contents> | 167 <assert_contents> |
| 169 <has_text text=">g1k_0"/> | 168 <has_text text=">g1k_0"/> |
| 170 </assert_contents> | 169 </assert_contents> |
| 171 </element> | 170 </element> |
| 172 <element name="1" ftype="fasta"> | 171 <element name="1" ftype="fasta"> |
| 173 <assert_contents> | 172 <assert_contents> |
| 173 <has_text text=">g1k_1"/> | |
| 174 </assert_contents> | |
| 175 </element> | |
| 176 <element name="2" ftype="fasta"> | |
| 177 <assert_contents> | |
| 178 <has_text text=">g1k_2"/> | |
| 179 </assert_contents> | |
| 180 </element> | |
| 181 <element name="39" ftype="fasta"> | |
| 182 <assert_contents> | |
| 183 <has_text text=">g3k_9"/> | |
| 184 </assert_contents> | |
| 185 </element> | |
| 186 </output_collection> | |
| 187 <output_collection name="output_bins" count="0"> | |
| 188 <!--<element name="0" ftype="fasta"> | |
| 189 <assert_contents> | |
| 190 <has_text text=">g1k_0"/> | |
| 191 </assert_contents> | |
| 192 </element> | |
| 193 <element name="1" ftype="fasta"> | |
| 194 <assert_contents> | |
| 174 <has_text text=">g2k_0"/> | 195 <has_text text=">g2k_0"/> |
| 175 </assert_contents> | 196 </assert_contents> |
| 176 </element> | 197 </element> |
| 177 <element name="2" ftype="fasta"> | 198 <element name="2" ftype="fasta"> |
| 178 <assert_contents> | 199 <assert_contents> |
| 179 <has_text text=">g3k_0"/> | 200 <has_text text=">g3k_0"/> |
| 180 </assert_contents> | 201 </assert_contents> |
| 181 </element> | 202 </element>--> |
| 182 </output_collection> | 203 </output_collection> |
| 183 <output name="single_data" ftype="csv"> | 204 <output name="single_data" ftype="csv"> |
| 184 <assert_contents> | 205 <assert_contents> |
| 185 <has_text text="g1k_0"/> | 206 <has_text text="g1k_0"/> |
| 186 <has_text text="g4k_7"/> | 207 <has_text text="g4k_7"/> |
| 290 <has_text text="g2k_7_2"/> | 311 <has_text text="g2k_7_2"/> |
| 291 </assert_contents> | 312 </assert_contents> |
| 292 </element> | 313 </element> |
| 293 </output_collection> | 314 </output_collection> |
| 294 </test> | 315 </test> |
| 316 <test expect_num_outputs="4"> | |
| 317 <conditional name="mode"> | |
| 318 <param name="select" value="co"/> | |
| 319 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> | |
| 320 <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/> | |
| 321 <conditional name="ref"> | |
| 322 <param name="select" value="taxonomy"/> | |
| 323 <param name="taxonomy_annotation_table" value="taxonomy.tsv"/> | |
| 324 </conditional> | |
| 325 </conditional> | |
| 326 <conditional name="min_len"> | |
| 327 <param name="method" value="ratio"/> | |
| 328 <param name="ratio" value="0.05"/> | |
| 329 </conditional> | |
| 330 <param name="orf_finder" value="fraggenescan"/> | |
| 331 <param name="random-seed" value="0"/> | |
| 332 <section name="annot"> | |
| 333 <param name="ml_threshold" value=""/> | |
| 334 </section> | |
| 335 <section name="training"> | |
| 336 <param name="epoches" value="20"/> | |
| 337 <param name="batch_size" value="2048"/> | |
| 338 </section> | |
| 339 <section name="bin"> | |
| 340 <param name="max_node" value="1"/> | |
| 341 <param name="max_edges" value="200"/> | |
| 342 <param name="minfasta_kbs" value="200"/> | |
| 343 <param name="no_recluster" value="false"/> | |
| 344 </section> | |
| 345 <param name="extra_output" value="coverage"/> | |
| 346 <output_collection name="output_recluster_bins" count="1"> | |
| 347 <element name="30" ftype="fasta"> | |
| 348 <assert_contents> | |
| 349 <has_text text=">g3k_0"/> | |
| 350 </assert_contents> | |
| 351 </element> | |
| 352 </output_collection> | |
| 353 <output_collection name="co_cov" count="5"> | |
| 354 <element name="0" ftype="csv"> | |
| 355 <assert_contents> | |
| 356 <has_text text="g1k_0"/> | |
| 357 <has_text text="g2k_7"/> | |
| 358 </assert_contents> | |
| 359 </element> | |
| 360 <element name="1" ftype="csv"> | |
| 361 <assert_contents> | |
| 362 <has_text text="g1k_0"/> | |
| 363 <has_text text="g2k_7"/> | |
| 364 </assert_contents> | |
| 365 </element> | |
| 366 <element name="4" ftype="csv"> | |
| 367 <assert_contents> | |
| 368 <has_text text="g1k_0"/> | |
| 369 <has_text text="g2k_7"/> | |
| 370 </assert_contents> | |
| 371 </element> | |
| 372 </output_collection> | |
| 373 <output_collection name="co_split_cov" count="5"> | |
| 374 <element name="0" ftype="csv"> | |
| 375 <assert_contents> | |
| 376 <has_text text="g1k_0_1"/> | |
| 377 <has_text text="g2k_7_2"/> | |
| 378 </assert_contents> | |
| 379 </element> | |
| 380 <element name="1" ftype="csv"> | |
| 381 <assert_contents> | |
| 382 <has_text text="g1k_0_1"/> | |
| 383 <has_text text="g2k_7_2"/> | |
| 384 </assert_contents> | |
| 385 </element> | |
| 386 <element name="2" ftype="csv"> | |
| 387 <assert_contents> | |
| 388 <has_text text="g1k_0_1"/> | |
| 389 <has_text text="g2k_7_2"/> | |
| 390 </assert_contents> | |
| 391 </element> | |
| 392 </output_collection> | |
| 393 </test> | |
| 295 <test expect_num_outputs="1"> | 394 <test expect_num_outputs="1"> |
| 296 <conditional name="mode"> | 395 <conditional name="mode"> |
| 297 <param name="select" value="single"/> | 396 <param name="select" value="single"/> |
| 298 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> | 397 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> |
| 299 <param name="input_bam" ftype="bam" value="input_single.bam"/> | 398 <param name="input_bam" ftype="bam" value="input_single.bam"/> |
| 328 <has_text text=">g1k_0"/> | 427 <has_text text=">g1k_0"/> |
| 329 </assert_contents> | 428 </assert_contents> |
| 330 </element> | 429 </element> |
| 331 </output_collection> | 430 </output_collection> |
| 332 </test> | 431 </test> |
| 432 <test expect_num_outputs="2"> | |
| 433 <conditional name="mode"> | |
| 434 <param name="select" value="single"/> | |
| 435 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> | |
| 436 <param name="input_bam" ftype="bam" value="input_single.bam"/> | |
| 437 <conditional name="ref"> | |
| 438 <param name="db_selector" value="cached"/> | |
| 439 <param name="cached_db" value="test-db"/> | |
| 440 </conditional> | |
| 441 </conditional> | |
| 442 <conditional name="min_len"> | |
| 443 <param name="method" value="ratio"/> | |
| 444 <param name="ratio" value="0.05"/> | |
| 445 </conditional> | |
| 446 <param name="orf_finder" value="fraggenescan"/> | |
| 447 <param name="random-seed" value="0"/> | |
| 448 <section name="annot"> | |
| 449 <param name="ml_threshold" value=""/> | |
| 450 </section> | |
| 451 <section name="training"> | |
| 452 <param name="epoches" value="20"/> | |
| 453 <param name="batch_size" value="2048"/> | |
| 454 </section> | |
| 455 <section name="bin"> | |
| 456 <param name="max_node" value="1"/> | |
| 457 <param name="max_edges" value="200"/> | |
| 458 <param name="minfasta_kbs" value="200"/> | |
| 459 <param name="no_recluster" value="false"/> | |
| 460 </section> | |
| 461 <param name="extra_output" value=""/> | |
| 462 <output_collection name="output_recluster_bins" count="1"> | |
| 463 <element name="30" ftype="fasta"> | |
| 464 <assert_contents> | |
| 465 <has_text text=">g3k_0"/> | |
| 466 </assert_contents> | |
| 467 </element> | |
| 468 </output_collection> | |
| 469 </test> | |
| 333 <test expect_num_outputs="8"> | 470 <test expect_num_outputs="8"> |
| 334 <conditional name="mode"> | 471 <conditional name="mode"> |
| 335 <param name="select" value="multi"/> | 472 <param name="select" value="multi"/> |
| 336 <conditional name="multi_fasta"> | 473 <conditional name="multi_fasta"> |
| 337 <param name="select" value="concatenated"/> | 474 <param name="select" value="concatenated"/> |
| 418 <has_text text=">g1k_0"/> | 555 <has_text text=">g1k_0"/> |
| 419 </assert_contents> | 556 </assert_contents> |
| 420 </element> | 557 </element> |
| 421 </output_collection> | 558 </output_collection> |
| 422 </test> | 559 </test> |
| 560 | |
| 423 </tests> | 561 </tests> |
| 424 <help><![CDATA[ | 562 <help><![CDATA[ |
| 425 @HELP_HEADER@ | 563 @HELP_HEADER@ |
| 426 | 564 |
| 427 Inputs | 565 Inputs |