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comparison minimap2.xml @ 20:bb2c5a19ecbd draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit c8aee6bdc2b4254df523c05890b4e3c4de5928f8"
author iuc
date Fri, 11 Jun 2021 21:39:25 +0000
parents 11ef1ee4282c
children 597f238f2b4d
comparison
equal deleted inserted replaced
19:11ef1ee4282c 20:bb2c5a19ecbd
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="edam_ontology"/> 7 <expand macro="edam_ontology"/>
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <expand macro="pe_anaylsis_fixed_selector"/>
10 <stdio> 9 <stdio>
11 <exit_code range="1:" level="fatal" /> 10 <exit_code range="1:" level="fatal" />
12 <regex match="\[ERROR\]" source="stderr" level="fatal" /> 11 <regex match="\[ERROR\]" source="stderr" level="fatal" />
13 </stdio> 12 </stdio>
14 <version_command>minimap2 --version</version_command> 13 <version_command>minimap2 --version</version_command>
145 #else if $fastq_input.fastq_input_selector == 'paired': 144 #else if $fastq_input.fastq_input_selector == 'paired':
146 '$fastq_input.fastq_input1' '$fastq_input.fastq_input2' 145 '$fastq_input.fastq_input1' '$fastq_input.fastq_input2'
147 #else if $fastq_input.fastq_input_selector == 'paired_collection': 146 #else if $fastq_input.fastq_input_selector == 'paired_collection':
148 '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse' 147 '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse'
149 #end if 148 #end if
149 #if str($io_options.output_format) in ('BAM', 'CRAM'):
150 -a | samtools view --no-PG -hT reference.fa
151 #end if
150 #if $io_options.output_format == 'BAM': 152 #if $io_options.output_format == 'BAM':
151 -a
152 | samtools sort 153 | samtools sort
153 -@\${GALAXY_SLOTS:-2} 154 -@\${GALAXY_SLOTS:-2}
154 -T "\${TMPDIR:-.}" 155 -T "\${TMPDIR:-.}"
155 -O $io_options.output_format 156 -O $io_options.output_format
156 -o '$alignment_output' 157 -o '$alignment_output'
157 #else if $io_options.output_format == 'CRAM': 158 #else if $io_options.output_format == 'CRAM':
158 -a
159 | samtools sort 159 | samtools sort
160 -T "\${TMPDIR:-.}" 160 -T "\${TMPDIR:-.}"
161 -@\${GALAXY_SLOTS:-2} 161 -@\${GALAXY_SLOTS:-2}
162 -O $io_options.output_format 162 -O $io_options.output_format
163 $io_options.eqx 163 $io_options.eqx
395 <param name="reference_source_selector" value="history" /> 395 <param name="reference_source_selector" value="history" />
396 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 396 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
397 <param name="fastq_input_selector" value="single"/> 397 <param name="fastq_input_selector" value="single"/>
398 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> 398 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
399 <param name="analysis_type_selector" value="sr"/> 399 <param name="analysis_type_selector" value="sr"/>
400 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" /> 400 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
401 </test> 401 </test>
402 <test> 402 <test>
403 <!-- test cram output --> 403 <!-- test cram output -->
404 <param name="reference_source_selector" value="history" /> 404 <param name="reference_source_selector" value="history" />
405 <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"/>
414 <param name="reference_source_selector" value="history" /> 414 <param name="reference_source_selector" value="history" />
415 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 415 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
416 <param name="fastq_input_selector" value="paired"/> 416 <param name="fastq_input_selector" value="paired"/>
417 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> 417 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
418 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> 418 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
419 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="2" /> 419 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
420 </test> 420 </test>
421 <test> 421 <test>
422 <!-- test paired input with one pair compressed --> 422 <!-- test paired input with one pair compressed -->
423 <param name="reference_source_selector" value="history" /> 423 <param name="reference_source_selector" value="history" />
424 <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"/>
425 <param name="fastq_input_selector" value="paired"/> 425 <param name="fastq_input_selector" value="paired"/>
426 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/> 426 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
427 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> 427 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
428 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="2" /> 428 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" />
429 </test> 429 </test>
430 <test> 430 <test>
431 <!-- test collection input --> 431 <!-- test collection input -->
432 <param name="reference_source_selector" value="history" /> 432 <param name="reference_source_selector" value="history" />
433 <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"/>
436 <collection type="paired"> 436 <collection type="paired">
437 <element name="forward" value="bwa-mem-fastq1.fq" /> 437 <element name="forward" value="bwa-mem-fastq1.fq" />
438 <element name="reverse" value="bwa-mem-fastq2.fq" /> 438 <element name="reverse" value="bwa-mem-fastq2.fq" />
439 </collection> 439 </collection>
440 </param> 440 </param>
441 <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="2" /> 441 <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="4" />
442 </test> 442 </test>
443 <test> 443 <test>
444 <!-- test data table reference --> 444 <!-- test data table reference -->
445 <param name="reference_source_selector" value="cached" /> 445 <param name="reference_source_selector" value="cached" />
446 <param name="ref_file" value="bwa-mem-mt-genome"/> 446 <param name="ref_file" value="bwa-mem-mt-genome"/>
447 <param name="fastq_input_selector" value="single"/> 447 <param name="fastq_input_selector" value="single"/>
448 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> 448 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
449 <param name="analysis_type_selector" value="sr"/> 449 <param name="analysis_type_selector" value="sr"/>
450 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" /> 450 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
451 </test> 451 </test>
452 <test> 452 <test>
453 <!-- test alignment options --> 453 <!-- test alignment options -->
454 <param name="reference_source_selector" value="cached" /> 454 <param name="reference_source_selector" value="cached" />
455 <param name="min_occ_floor" value="1000"/> 455 <param name="min_occ_floor" value="1000"/>
468 <param name="E" value="2" /> 468 <param name="E" value="2" />
469 <param name="E2" value="1" /> 469 <param name="E2" value="1" />
470 <param name="z" value="400" /> 470 <param name="z" value="400" />
471 <param name="s" value="40" /> 471 <param name="s" value="40" />
472 </section> 472 </section>
473 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" /> 473 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" />
474 </test> 474 </test>
475 <test> 475 <test>
476 <!-- test paf output --> 476 <!-- test paf output -->
477 <param name="reference_source_selector" value="history" /> 477 <param name="reference_source_selector" value="history" />
478 <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" /> 478 <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" />
487 <param name="reference_source_selector" value="history" /> 487 <param name="reference_source_selector" value="history" />
488 <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" /> 488 <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" />
489 <param name="fastq_input_selector" value="single" /> 489 <param name="fastq_input_selector" value="single" />
490 <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" /> 490 <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" />
491 <param name="analysis_type_selector" value="self-homology" /> 491 <param name="analysis_type_selector" value="self-homology" />
492 <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="2" /> 492 <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="4" />
493 </test> 493 </test>
494 <test> 494 <test>
495 <!-- test mask-len option --> 495 <!-- test mask-len option -->
496 <param name="reference_source_selector" value="history" /> 496 <param name="reference_source_selector" value="history" />
497 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 497 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
499 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> 499 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
500 <param name="analysis_type_selector" value="sr"/> 500 <param name="analysis_type_selector" value="sr"/>
501 <section name="mapping_options"> 501 <section name="mapping_options">
502 <param name="mask_len" value="100"/> 502 <param name="mask_len" value="100"/>
503 </section> 503 </section>
504 <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="2" /> 504 <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="4" />
505 </test> 505 </test>
506 <test> 506 <test>
507 <!-- test map-hifi --> 507 <!-- test map-hifi -->
508 <param name="reference_source_selector" value="history" /> 508 <param name="reference_source_selector" value="history" />
509 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa.gz"/> 509 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa.gz"/>
510 <param name="fastq_input_selector" value="single"/> 510 <param name="fastq_input_selector" value="single"/>
511 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/> 511 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/>
512 <param name="analysis_type_selector" value="map-hifi"/> 512 <param name="analysis_type_selector" value="map-hifi"/>
513 <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="2" /> 513 <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" />
514 </test> 514 </test>
515 <test> 515 <test>
516 <!-- test kmer ocurrence interval option --> 516 <!-- test kmer ocurrence interval option -->
517 <param name="reference_source_selector" value="history" /> 517 <param name="reference_source_selector" value="history" />
518 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 518 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
522 <conditional name="kmer_ocurrence_interval"> 522 <conditional name="kmer_ocurrence_interval">
523 <param name="interval" value="enabled"/> 523 <param name="interval" value="enabled"/>
524 <param name="lower_limit" value="10"/> 524 <param name="lower_limit" value="10"/>
525 <param name="upper_limit" value="30"/> 525 <param name="upper_limit" value="30"/>
526 </conditional> 526 </conditional>
527 <output name="alignment_output" ftype="bam" file="minimap2-test-kmer_ocurrence.bam" lines_diff="2" /> 527 <output name="alignment_output" ftype="bam" file="minimap2-test-kmer_ocurrence.bam" lines_diff="4" />
528 </test> 528 </test>
529 </tests> 529 </tests>
530 <help> 530 <help>
531 531
532 Users’ Guide 532 Users’ Guide