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comparison hifiasm.xml @ 8:5f625c63b8bc draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed
author bgruening
date Tue, 25 Oct 2022 18:13:16 +0000
parents 366a11d316a7
children c388a21dcbf1
comparison
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7:366a11d316a7 8:5f625c63b8bc
1 <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description> 2 <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.16.1</token> 4 <token name="@TOOL_VERSION@">0.16.1</token>
5 <token name="@VERSION_SUFFIX@">3</token> 5 <token name="@VERSION_SUFFIX@">4</token>
6 <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token> 6 <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>
7 <xml name="reads"> 7 <xml name="reads">
8 <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" /> 8 <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" />
9 </xml> 9 </xml>
10 </macros> 10 </macros>
129 --primary 129 --primary
130 $input_filenames 130 $input_filenames
131 #if $log_out: 131 #if $log_out:
132 2> output.log 132 2> output.log
133 #end if 133 #end if
134 && mkdir noseq_files && mv *.noseq.gfa noseq_files
134 ]]> 135 ]]>
135 </command> 136 </command>
136 <inputs> 137 <inputs>
137 <conditional name="mode"> 138 <conditional name="mode">
138 <param name="mode_selector" type="select" label="Assembly mode"> 139 <param name="mode_selector" type="select" label="Assembly mode">
290 </data> 291 </data>
291 <!--Log output--> 292 <!--Log output-->
292 <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}: log file"> 293 <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}: log file">
293 <filter>log_out</filter> 294 <filter>log_out</filter>
294 </data> 295 </data>
296 <collection name="noseq files" type="list" label="${tool.name} on ${on_string}: noseq files">
297 <discover_datasets pattern="__name_and_ext__" format="gfa1" directory="noseq_files" />
298 </collection>
295 </outputs> 299 </outputs>
296 <tests> 300 <tests>
297 <test expect_num_outputs="4"> 301 <test expect_num_outputs="5">
298 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 302 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
299 <param name="filter_bits" value="0" /> 303 <param name="filter_bits" value="0" />
300 <param name="mode_selector" value="standard" /> 304 <param name="mode_selector" value="standard" />
301 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" /> 305 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />
302 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" /> 306 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" />
305 <assert_contents> 309 <assert_contents>
306 <has_size value="0"/> 310 <has_size value="0"/>
307 </assert_contents> 311 </assert_contents>
308 </output> 312 </output>
309 </test> 313 </test>
310 <test expect_num_outputs="4"> 314 <test expect_num_outputs="5">
311 <param name="reads" value="hifiasm-in2-0.fa.gz,hifiasm-in2-1.fa.gz,hifiasm-in2-2.fa.gz,hifiasm-in2-3.fa.gz,hifiasm-in2-4.fa.gz" ftype="fasta.gz" /> 315 <param name="reads" value="hifiasm-in2-0.fa.gz,hifiasm-in2-1.fa.gz,hifiasm-in2-2.fa.gz,hifiasm-in2-3.fa.gz,hifiasm-in2-4.fa.gz" ftype="fasta.gz" />
312 <param name="filter_bits" value="0" /> 316 <param name="filter_bits" value="0" />
313 <param name="mode_selector" value="standard" /> 317 <param name="mode_selector" value="standard" />
314 <output name="raw_unitigs" file="hifiasm-out2-raw.gfa" ftype="gfa1" /> 318 <output name="raw_unitigs" file="hifiasm-out2-raw.gfa" ftype="gfa1" />
315 <output name="processed_unitigs" file="hifiasm-out2-processed.gfa" ftype="gfa1" /> 319 <output name="processed_unitigs" file="hifiasm-out2-processed.gfa" ftype="gfa1" />
319 <has_size value="0"/> 323 <has_size value="0"/>
320 </assert_contents> 324 </assert_contents>
321 </output> 325 </output>
322 </test> 326 </test>
323 <!-- Test logfile out--> 327 <!-- Test logfile out-->
324 <test expect_num_outputs="5"> 328 <test expect_num_outputs="6">
325 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 329 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
326 <param name="filter_bits" value="0" /> 330 <param name="filter_bits" value="0" />
327 <param name="mode_selector" value="standard" /> 331 <param name="mode_selector" value="standard" />
328 <param name="log_out" value="yes"/> 332 <param name="log_out" value="yes"/>
329 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" /> 333 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />
339 <has_line line="[M::main] CMD: hifiasm -t 1 -o output -f 0 --primary input_0.fasta.gz"/> 343 <has_line line="[M::main] CMD: hifiasm -t 1 -o output -f 0 --primary input_0.fasta.gz"/>
340 </assert_contents> 344 </assert_contents>
341 </output> 345 </output>
342 </test> 346 </test>
343 <!--Test Hi-C reads--> 347 <!--Test Hi-C reads-->
344 <test expect_num_outputs="5"> 348 <test expect_num_outputs="6">
345 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 349 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
346 <param name="filter_bits" value="0" /> 350 <param name="filter_bits" value="0" />
347 <param name="mode_selector" value="standard" /> 351 <param name="mode_selector" value="standard" />
348 <conditional name="hic_partition"> 352 <conditional name="hic_partition">
349 <param name="hic_partition_selector" value="set"/> 353 <param name="hic_partition_selector" value="set"/>
374 <has_size value="59522" delta="500"/> 378 <has_size value="59522" delta="500"/>
375 </assert_contents> 379 </assert_contents>
376 </output> 380 </output>
377 </test> 381 </test>
378 <!-- Test trio mode --> 382 <!-- Test trio mode -->
379 <test expect_num_outputs="4"> 383 <test expect_num_outputs="5">
380 <param name="filter_bits" value="0"/> 384 <param name="filter_bits" value="0"/>
381 <conditional name="mode"> 385 <conditional name="mode">
382 <param name="mode_selector" value="trio"/> 386 <param name="mode_selector" value="trio"/>
383 <param name="reads" value="child.fasta.gz"/> 387 <param name="reads" value="child.fasta.gz"/>
384 <param name="hap1_reads" value="paternal.fasta.gz"/> 388 <param name="hap1_reads" value="paternal.fasta.gz"/>
406 <has_size value="0"/> 410 <has_size value="0"/>
407 </assert_contents> 411 </assert_contents>
408 </output> 412 </output>
409 </test> 413 </test>
410 <!-- Test ignore-error-corrected option --> 414 <!-- Test ignore-error-corrected option -->
411 <test expect_num_outputs="4"> 415 <test expect_num_outputs="5">
412 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 416 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
413 <param name="filter_bits" value="0" /> 417 <param name="filter_bits" value="0" />
414 <param name="mode_selector" value="standard" /> 418 <param name="mode_selector" value="standard" />
415 <conditional name="assembly_options"> 419 <conditional name="assembly_options">
416 <param name="assembly_selector" value="set"/> 420 <param name="assembly_selector" value="set"/>
424 <has_size value="0"/> 428 <has_size value="0"/>
425 </assert_contents> 429 </assert_contents>
426 </output> 430 </output>
427 </test> 431 </test>
428 <!-- Test expected haplotype number --> 432 <!-- Test expected haplotype number -->
429 <test expect_num_outputs="4"> 433 <test expect_num_outputs="5">
430 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 434 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
431 <param name="filter_bits" value="0" /> 435 <param name="filter_bits" value="0" />
432 <param name="mode_selector" value="standard" /> 436 <param name="mode_selector" value="standard" />
433 <conditional name="purge_options"> 437 <conditional name="purge_options">
434 <param name="purge_selector" value="set"/> 438 <param name="purge_selector" value="set"/>
442 <has_size value="0"/> 446 <has_size value="0"/>
443 </assert_contents> 447 </assert_contents>
444 </output> 448 </output>
445 </test> 449 </test>
446 <!-- Test min_hist_cnt option --> 450 <!-- Test min_hist_cnt option -->
447 <test expect_num_outputs="4"> 451 <test expect_num_outputs="5">
448 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 452 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
449 <param name="filter_bits" value="0" /> 453 <param name="filter_bits" value="0" />
450 <param name="mode_selector" value="standard" /> 454 <param name="mode_selector" value="standard" />
451 <conditional name="advanced_options"> 455 <conditional name="advanced_options">
452 <param name="advanced_selector" value="set"/> 456 <param name="advanced_selector" value="set"/>
460 <has_size value="0"/> 464 <has_size value="0"/>
461 </assert_contents> 465 </assert_contents>
462 </output> 466 </output>
463 </test> 467 </test>
464 <!-- Test max_kooc option --> 468 <!-- Test max_kooc option -->
465 <test expect_num_outputs="4"> 469 <test expect_num_outputs="5">
466 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 470 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
467 <param name="filter_bits" value="0" /> 471 <param name="filter_bits" value="0" />
468 <param name="mode_selector" value="standard" /> 472 <param name="mode_selector" value="standard" />
469 <conditional name="advanced_options"> 473 <conditional name="advanced_options">
470 <param name="advanced_selector" value="set"/> 474 <param name="advanced_selector" value="set"/>
478 <has_size value="0"/> 482 <has_size value="0"/>
479 </assert_contents> 483 </assert_contents>
480 </output> 484 </output>
481 </test> 485 </test>
482 <!-- Test hg-size option --> 486 <!-- Test hg-size option -->
483 <test expect_num_outputs="4"> 487 <test expect_num_outputs="5">
484 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 488 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
485 <param name="filter_bits" value="0" /> 489 <param name="filter_bits" value="0" />
486 <param name="mode_selector" value="standard" /> 490 <param name="mode_selector" value="standard" />
487 <conditional name="advanced_options"> 491 <conditional name="advanced_options">
488 <param name="advanced_selector" value="set"/> 492 <param name="advanced_selector" value="set"/>
496 <has_size value="0"/> 500 <has_size value="0"/>
497 </assert_contents> 501 </assert_contents>
498 </output> 502 </output>
499 </test> 503 </test>
500 <!-- Test ignore-error-corrected option --> 504 <!-- Test ignore-error-corrected option -->
501 <test expect_num_outputs="4"> 505 <test expect_num_outputs="5">
502 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> 506 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
503 <param name="filter_bits" value="0" /> 507 <param name="filter_bits" value="0" />
504 <param name="mode_selector" value="standard" /> 508 <param name="mode_selector" value="standard" />
505 <conditional name="assembly_options"> 509 <conditional name="assembly_options">
506 <param name="assembly_selector" value="set"/> 510 <param name="assembly_selector" value="set"/>