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comparison minimap2.xml @ 28:f774b65c34d0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 980f7472892817697208792e4443fa579625b696
author iuc
date Tue, 04 Feb 2025 09:15:44 +0000
parents 068470a24bb5
children cbe067a674a9
comparison
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27:876749149e6d 28:f774b65c34d0
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> 2 <tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
3 <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description> 3 <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
4 <xrefs>
5 <xref type="bio.tools">minimap2</xref>
6 </xrefs>
7 <macros> 4 <macros>
8 <import>macros.xml</import> 5 <import>macros.xml</import>
9 </macros> 6 </macros>
10 <expand macro="edam_ontology"/> 7 <expand macro="edam_ontology"/>
8 <xrefs>
9 <xref type="bio.tools">minimap2</xref>
10 </xrefs>
11 <expand macro="requirements"/> 11 <expand macro="requirements"/>
12 <stdio> 12 <stdio>
13 <exit_code range="1:" level="fatal" /> 13 <exit_code range="1:" level="fatal" />
14 <regex match="\[ERROR\]" source="stderr" level="fatal" /> 14 <regex match="\[ERROR\]" source="stderr" level="fatal" />
15 </stdio> 15 </stdio>
139 #end if 139 #end if
140 $io_options.Y 140 $io_options.Y
141 #if $io_options.K: 141 #if $io_options.K:
142 -K $io_options.K 142 -K $io_options.K
143 #end if 143 #end if
144 #if $io_options.eqx:
145 --eqx
146 #end if
144 -t \${GALAXY_SLOTS:-4} 147 -t \${GALAXY_SLOTS:-4}
145 reference.fa 148 reference.fa
146 #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']: 149 #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
147 '$fastq_input.fastq_input1' 150 '$fastq_input.fastq_input1'
148 #else if $fastq_input.fastq_input_selector == 'paired': 151 #else if $fastq_input.fastq_input_selector == 'paired':
162 #else if $io_options.output_format == 'CRAM': 165 #else if $io_options.output_format == 'CRAM':
163 | samtools sort 166 | samtools sort
164 -T "\${TMPDIR:-.}" 167 -T "\${TMPDIR:-.}"
165 -@\${GALAXY_SLOTS:-2} 168 -@\${GALAXY_SLOTS:-2}
166 -O $io_options.output_format 169 -O $io_options.output_format
167 $io_options.eqx
168 --reference reference.fa 170 --reference reference.fa
169 --output-fmt-option no_ref 171 --output-fmt-option no_ref
170 -o '$alignment_output' 172 -o '$alignment_output'
171 #else: 173 #else:
172 > '$alignment_output' 174 > '$alignment_output'
235 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> 237 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
236 <expand macro="pe_anaylsis_fixed_selector" /> 238 <expand macro="pe_anaylsis_fixed_selector" />
237 </when> 239 </when>
238 </conditional> 240 </conditional>
239 <section name="indexing_options" title="Indexing options"> 241 <section name="indexing_options" title="Indexing options">
240 <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/> 242 <param argument="-H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>
241 <param argument="-k" type="integer" min="4" max="28" optional="true" label="K-mer size" help=""/> 243 <param argument="-k" type="integer" min="4" max="28" optional="true" label="K-mer size" help=""/>
242 <param argument="-w" type="integer" min="1" optional="true" label="Minimizer window size" help=""/> 244 <param argument="-w" type="integer" min="1" optional="true" label="Minimizer window size" help=""/>
243 <param argument="-I" type="integer" min="1" optional="true" label="Split index for every N input gigabases" help=""/> 245 <param argument="-I" type="integer" min="1" optional="true" label="Split index for every N input gigabases" help=""/>
244 </section> 246 </section>
245 <section name="mapping_options" title="Mapping options" help="Sets -f, -g, -F, -r, -n, -m, -X, -p, -N and --min-occ-floor options." expanded="False"> 247 <section name="mapping_options" title="Mapping options" help="Sets -f, -g, -F, -r, -n, -m, -X, -p, -N and --min-occ-floor options." expanded="False">
395 <when input="io_options.output_format" value="CRAM" format="cram" /> 397 <when input="io_options.output_format" value="CRAM" format="cram" />
396 </change_format> 398 </change_format>
397 </data> 399 </data>
398 </outputs> 400 </outputs>
399 <tests> 401 <tests>
400 <test> 402 <test expect_num_outputs="1">
401 <!-- test single input --> 403 <!-- test single input -->
402 <param name="reference_source_selector" value="history" /> 404 <param name="reference_source_selector" value="history" />
403 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 405 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
404 <param name="fastq_input_selector" value="single"/> 406 <param name="fastq_input_selector" value="single"/>
405 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> 407 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
406 <param name="analysis_type_selector" value="sr"/> 408 <param name="analysis_type_selector" value="sr"/>
407 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" /> 409 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
408 </test> 410 </test>
409 <test> 411 <test expect_num_outputs="1">
410 <!-- test cram output --> 412 <!-- test cram output -->
411 <param name="reference_source_selector" value="history" /> 413 <param name="reference_source_selector" value="history" />
412 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 414 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
413 <param name="fastq_input_selector" value="single"/> 415 <param name="fastq_input_selector" value="single"/>
414 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> 416 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
415 <param name="analysis_type_selector" value="sr"/> 417 <param name="analysis_type_selector" value="sr"/>
416 <param name="output_format" value="CRAM"/> 418 <param name="output_format" value="CRAM"/>
417 <output name="alignment_output" ftype="cram" file="minimap2-test1-fasta.cram" compare="sim_size" /> 419 <output name="alignment_output" ftype="cram" file="minimap2-test1-fasta.cram" compare="sim_size" />
418 </test> 420 </test>
419 <test> 421 <test expect_num_outputs="1">
420 <!-- test paired input --> 422 <!-- test paired input -->
421 <param name="reference_source_selector" value="history" /> 423 <param name="reference_source_selector" value="history" />
422 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 424 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
423 <param name="fastq_input_selector" value="paired"/> 425 <param name="fastq_input_selector" value="paired"/>
424 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> 426 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
425 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> 427 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
426 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" /> 428 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
427 </test> 429 </test>
428 <test> 430 <test expect_num_outputs="1">
429 <!-- test paired input with one pair compressed --> 431 <!-- test paired input with one pair compressed -->
430 <param name="reference_source_selector" value="history" /> 432 <param name="reference_source_selector" value="history" />
431 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 433 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
432 <param name="fastq_input_selector" value="paired"/> 434 <param name="fastq_input_selector" value="paired"/>
433 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/> 435 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
434 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> 436 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
435 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" /> 437 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
436 </test> 438 </test>
437 <test> 439 <test expect_num_outputs="1">
438 <!-- test collection input --> 440 <!-- test collection input -->
439 <param name="reference_source_selector" value="history" /> 441 <param name="reference_source_selector" value="history" />
440 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 442 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
441 <param name="fastq_input_selector" value="paired_collection"/> 443 <param name="fastq_input_selector" value="paired_collection"/>
442 <param name="fastq_input1"> 444 <param name="fastq_input1">
445 <element name="reverse" value="bwa-mem-fastq2.fq" /> 447 <element name="reverse" value="bwa-mem-fastq2.fq" />
446 </collection> 448 </collection>
447 </param> 449 </param>
448 <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="4" /> 450 <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="4" />
449 </test> 451 </test>
450 <test> 452 <test expect_num_outputs="1">
451 <!-- test data table reference --> 453 <!-- test data table reference -->
452 <param name="reference_source_selector" value="cached" /> 454 <param name="reference_source_selector" value="cached" />
453 <param name="ref_file" value="bwa-mem-mt-genome"/> 455 <param name="ref_file" value="bwa-mem-mt-genome"/>
454 <param name="fastq_input_selector" value="single"/> 456 <param name="fastq_input_selector" value="single"/>
455 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> 457 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
456 <param name="analysis_type_selector" value="sr"/> 458 <param name="analysis_type_selector" value="sr"/>
457 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" /> 459 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
458 </test> 460 </test>
459 <test> 461 <test expect_num_outputs="1">
460 <!-- test alignment options --> 462 <!-- test alignment options -->
461 <param name="reference_source_selector" value="cached" /> 463 <param name="reference_source_selector" value="cached" />
462 <param name="min_occ_floor" value="1000"/> 464 <param name="min_occ_floor" value="1000"/>
463 <param name="ref_file" value="bwa-mem-mt-genome"/> 465 <param name="ref_file" value="bwa-mem-mt-genome"/>
464 <param name="fastq_input_selector" value="single"/> 466 <param name="fastq_input_selector" value="single"/>
482 a valid command line is formed for the cs option --> 484 a valid command line is formed for the cs option -->
483 <param name="cs" value="none" /> 485 <param name="cs" value="none" />
484 </section> 486 </section>
485 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" /> 487 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
486 </test> 488 </test>
487 <test> 489 <test expect_num_outputs="1">
488 <!-- test paf output --> 490 <!-- test paf output -->
489 <param name="reference_source_selector" value="history" /> 491 <param name="reference_source_selector" value="history" />
490 <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" /> 492 <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" />
491 <param name="fastq_input_selector" value="single"/> 493 <param name="fastq_input_selector" value="single"/>
492 <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" /> 494 <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" />
493 <param name="analysis_type_selector" value="ava-ont"/> 495 <param name="analysis_type_selector" value="ava-ont"/>
494 <param name="output_format" value="paf"/> 496 <param name="output_format" value="paf"/>
495 <output name="alignment_output" ftype="paf" file="mini_reads.paf" /> 497 <output name="alignment_output" ftype="paf" file="mini_reads.paf" />
496 </test> 498 </test>
497 <test> 499 <test expect_num_outputs="1">
498 <!-- test self-homology mode --> 500 <!-- test self-homology mode -->
499 <param name="reference_source_selector" value="history" /> 501 <param name="reference_source_selector" value="history" />
500 <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" /> 502 <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" />
501 <param name="fastq_input_selector" value="single" /> 503 <param name="fastq_input_selector" value="single" />
502 <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" /> 504 <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" />
503 <param name="analysis_type_selector" value="self-homology" /> 505 <param name="analysis_type_selector" value="self-homology" />
504 <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="4" /> 506 <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="4" />
505 </test> 507 </test>
506 <test> 508 <test expect_num_outputs="1">
507 <!-- test mask-len option --> 509 <!-- test mask-len option -->
508 <param name="reference_source_selector" value="history" /> 510 <param name="reference_source_selector" value="history" />
509 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 511 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
510 <param name="fastq_input_selector" value="single"/> 512 <param name="fastq_input_selector" value="single"/>
511 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> 513 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
513 <section name="mapping_options"> 515 <section name="mapping_options">
514 <param name="mask_len" value="100"/> 516 <param name="mask_len" value="100"/>
515 </section> 517 </section>
516 <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="4" /> 518 <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="4" />
517 </test> 519 </test>
518 <test> 520 <test expect_num_outputs="1">
519 <!-- test map-hifi --> 521 <!-- test map-hifi -->
520 <param name="reference_source_selector" value="history" /> 522 <param name="reference_source_selector" value="history" />
521 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa.gz"/> 523 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa.gz"/>
522 <param name="fastq_input_selector" value="single"/> 524 <param name="fastq_input_selector" value="single"/>
523 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/> 525 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>
524 <param name="analysis_type_selector" value="map-hifi"/> 526 <param name="analysis_type_selector" value="map-hifi"/>
525 <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" /> 527 <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" />
526 </test> 528 </test>
527 <test> 529 <test expect_num_outputs="1">
528 <!-- test map-hifi uncompressed reference--> 530 <!-- test map-hifi uncompressed reference-->
529 <param name="reference_source_selector" value="history" /> 531 <param name="reference_source_selector" value="history" />
530 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa"/> 532 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa"/>
531 <param name="fastq_input_selector" value="single"/> 533 <param name="fastq_input_selector" value="single"/>
532 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/> 534 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>
533 <param name="analysis_type_selector" value="map-hifi"/> 535 <param name="analysis_type_selector" value="map-hifi"/>
534 <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-2-fasta.bam" lines_diff="4" /> 536 <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-2-fasta.bam" lines_diff="4" />
535 </test> 537 </test>
536 <test> 538 <test expect_num_outputs="1">
537 <!-- test kmer ocurrence interval option --> 539 <!-- test kmer ocurrence interval option -->
538 <param name="reference_source_selector" value="history" /> 540 <param name="reference_source_selector" value="history" />
539 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 541 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
540 <param name="fastq_input_selector" value="single"/> 542 <param name="fastq_input_selector" value="single"/>
541 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> 543 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>