Mercurial > repos > iuc > minimap2
comparison minimap2.xml @ 20:92678fcb1a5f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 20bce2a5482efb97b9176bfceeb527ef36ddbe4b
| author | iuc |
|---|---|
| date | Mon, 18 Mar 2024 16:43:36 +0000 |
| parents | c0c2d0941de8 |
| children |
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| 19:be1d967337e4 | 20:92678fcb1a5f |
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| 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> |
| 235 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> | 235 <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" /> | 236 <expand macro="pe_anaylsis_fixed_selector" /> |
| 237 </when> | 237 </when> |
| 238 </conditional> | 238 </conditional> |
| 239 <section name="indexing_options" title="Indexing options"> | 239 <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 ?"/> | 240 <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=""/> | 241 <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=""/> | 242 <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=""/> | 243 <param argument="-I" type="integer" min="1" optional="true" label="Split index for every N input gigabases" help=""/> |
| 244 </section> | 244 </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"> | 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"> |
| 395 <when input="io_options.output_format" value="CRAM" format="cram" /> | 395 <when input="io_options.output_format" value="CRAM" format="cram" /> |
| 396 </change_format> | 396 </change_format> |
| 397 </data> | 397 </data> |
| 398 </outputs> | 398 </outputs> |
| 399 <tests> | 399 <tests> |
| 400 <test> | 400 <test expect_num_outputs="1"> |
| 401 <!-- test single input --> | 401 <!-- test single input --> |
| 402 <param name="reference_source_selector" value="history" /> | 402 <param name="reference_source_selector" value="history" /> |
| 403 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> | 403 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
| 404 <param name="fastq_input_selector" value="single"/> | 404 <param name="fastq_input_selector" value="single"/> |
| 405 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> | 405 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> |
| 406 <param name="analysis_type_selector" value="sr"/> | 406 <param name="analysis_type_selector" value="sr"/> |
| 407 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" /> | 407 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" /> |
| 408 </test> | 408 </test> |
| 409 <test> | 409 <test expect_num_outputs="1"> |
| 410 <!-- test cram output --> | 410 <!-- test cram output --> |
| 411 <param name="reference_source_selector" value="history" /> | 411 <param name="reference_source_selector" value="history" /> |
| 412 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> | 412 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
| 413 <param name="fastq_input_selector" value="single"/> | 413 <param name="fastq_input_selector" value="single"/> |
| 414 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> | 414 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> |
| 415 <param name="analysis_type_selector" value="sr"/> | 415 <param name="analysis_type_selector" value="sr"/> |
| 416 <param name="output_format" value="CRAM"/> | 416 <param name="output_format" value="CRAM"/> |
| 417 <output name="alignment_output" ftype="cram" file="minimap2-test1-fasta.cram" compare="sim_size" /> | 417 <output name="alignment_output" ftype="cram" file="minimap2-test1-fasta.cram" compare="sim_size" /> |
| 418 </test> | 418 </test> |
| 419 <test> | 419 <test expect_num_outputs="1"> |
| 420 <!-- test paired input --> | 420 <!-- test paired input --> |
| 421 <param name="reference_source_selector" value="history" /> | 421 <param name="reference_source_selector" value="history" /> |
| 422 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> | 422 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
| 423 <param name="fastq_input_selector" value="paired"/> | 423 <param name="fastq_input_selector" value="paired"/> |
| 424 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> | 424 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> |
| 425 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> | 425 <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" /> | 426 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" /> |
| 427 </test> | 427 </test> |
| 428 <test> | 428 <test expect_num_outputs="1"> |
| 429 <!-- test paired input with one pair compressed --> | 429 <!-- test paired input with one pair compressed --> |
| 430 <param name="reference_source_selector" value="history" /> | 430 <param name="reference_source_selector" value="history" /> |
| 431 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> | 431 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
| 432 <param name="fastq_input_selector" value="paired"/> | 432 <param name="fastq_input_selector" value="paired"/> |
| 433 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/> | 433 <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"/> | 434 <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" /> | 435 <output name="alignment_output" ftype="bam" file="minimap2-test1.bam" lines_diff="4" /> |
| 436 </test> | 436 </test> |
| 437 <test> | 437 <test expect_num_outputs="1"> |
| 438 <!-- test collection input --> | 438 <!-- test collection input --> |
| 439 <param name="reference_source_selector" value="history" /> | 439 <param name="reference_source_selector" value="history" /> |
| 440 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> | 440 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
| 441 <param name="fastq_input_selector" value="paired_collection"/> | 441 <param name="fastq_input_selector" value="paired_collection"/> |
| 442 <param name="fastq_input1"> | 442 <param name="fastq_input1"> |
| 445 <element name="reverse" value="bwa-mem-fastq2.fq" /> | 445 <element name="reverse" value="bwa-mem-fastq2.fq" /> |
| 446 </collection> | 446 </collection> |
| 447 </param> | 447 </param> |
| 448 <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="4" /> | 448 <output name="alignment_output" ftype="bam" file="minimap2-test2.bam" lines_diff="4" /> |
| 449 </test> | 449 </test> |
| 450 <test> | 450 <test expect_num_outputs="1"> |
| 451 <!-- test data table reference --> | 451 <!-- test data table reference --> |
| 452 <param name="reference_source_selector" value="cached" /> | 452 <param name="reference_source_selector" value="cached" /> |
| 453 <param name="ref_file" value="bwa-mem-mt-genome"/> | 453 <param name="ref_file" value="bwa-mem-mt-genome"/> |
| 454 <param name="fastq_input_selector" value="single"/> | 454 <param name="fastq_input_selector" value="single"/> |
| 455 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> | 455 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> |
| 456 <param name="analysis_type_selector" value="sr"/> | 456 <param name="analysis_type_selector" value="sr"/> |
| 457 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" /> | 457 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" /> |
| 458 </test> | 458 </test> |
| 459 <test> | 459 <test expect_num_outputs="1"> |
| 460 <!-- test alignment options --> | 460 <!-- test alignment options --> |
| 461 <param name="reference_source_selector" value="cached" /> | 461 <param name="reference_source_selector" value="cached" /> |
| 462 <param name="min_occ_floor" value="1000"/> | 462 <param name="min_occ_floor" value="1000"/> |
| 463 <param name="ref_file" value="bwa-mem-mt-genome"/> | 463 <param name="ref_file" value="bwa-mem-mt-genome"/> |
| 464 <param name="fastq_input_selector" value="single"/> | 464 <param name="fastq_input_selector" value="single"/> |
| 482 a valid command line is formed for the cs option --> | 482 a valid command line is formed for the cs option --> |
| 483 <param name="cs" value="none" /> | 483 <param name="cs" value="none" /> |
| 484 </section> | 484 </section> |
| 485 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" /> | 485 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="4" /> |
| 486 </test> | 486 </test> |
| 487 <test> | 487 <test expect_num_outputs="1"> |
| 488 <!-- test paf output --> | 488 <!-- test paf output --> |
| 489 <param name="reference_source_selector" value="history" /> | 489 <param name="reference_source_selector" value="history" /> |
| 490 <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" /> | 490 <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" /> |
| 491 <param name="fastq_input_selector" value="single"/> | 491 <param name="fastq_input_selector" value="single"/> |
| 492 <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" /> | 492 <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" /> |
| 493 <param name="analysis_type_selector" value="ava-ont"/> | 493 <param name="analysis_type_selector" value="ava-ont"/> |
| 494 <param name="output_format" value="paf"/> | 494 <param name="output_format" value="paf"/> |
| 495 <output name="alignment_output" ftype="paf" file="mini_reads.paf" /> | 495 <output name="alignment_output" ftype="paf" file="mini_reads.paf" /> |
| 496 </test> | 496 </test> |
| 497 <test> | 497 <test expect_num_outputs="1"> |
| 498 <!-- test self-homology mode --> | 498 <!-- test self-homology mode --> |
| 499 <param name="reference_source_selector" value="history" /> | 499 <param name="reference_source_selector" value="history" /> |
| 500 <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" /> | 500 <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" /> |
| 501 <param name="fastq_input_selector" value="single" /> | 501 <param name="fastq_input_selector" value="single" /> |
| 502 <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" /> | 502 <param name="fastq_input1" ftype="fasta" value="minimap2-self-homology.fasta" /> |
| 503 <param name="analysis_type_selector" value="self-homology" /> | 503 <param name="analysis_type_selector" value="self-homology" /> |
| 504 <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="4" /> | 504 <output name="alignment_output" ftype="bam" file="minimap2-self-homology.bam" lines_diff="4" /> |
| 505 </test> | 505 </test> |
| 506 <test> | 506 <test expect_num_outputs="1"> |
| 507 <!-- test mask-len option --> | 507 <!-- test mask-len option --> |
| 508 <param name="reference_source_selector" value="history" /> | 508 <param name="reference_source_selector" value="history" /> |
| 509 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> | 509 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
| 510 <param name="fastq_input_selector" value="single"/> | 510 <param name="fastq_input_selector" value="single"/> |
| 511 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> | 511 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> |
| 513 <section name="mapping_options"> | 513 <section name="mapping_options"> |
| 514 <param name="mask_len" value="100"/> | 514 <param name="mask_len" value="100"/> |
| 515 </section> | 515 </section> |
| 516 <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="4" /> | 516 <output name="alignment_output" ftype="bam" file="minimap2-test-mask_len.bam" lines_diff="4" /> |
| 517 </test> | 517 </test> |
| 518 <test> | 518 <test expect_num_outputs="1"> |
| 519 <!-- test map-hifi --> | 519 <!-- test map-hifi --> |
| 520 <param name="reference_source_selector" value="history" /> | 520 <param name="reference_source_selector" value="history" /> |
| 521 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa.gz"/> | 521 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa.gz"/> |
| 522 <param name="fastq_input_selector" value="single"/> | 522 <param name="fastq_input_selector" value="single"/> |
| 523 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/> | 523 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/> |
| 524 <param name="analysis_type_selector" value="map-hifi"/> | 524 <param name="analysis_type_selector" value="map-hifi"/> |
| 525 <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" /> | 525 <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" /> |
| 526 </test> | 526 </test> |
| 527 <test> | 527 <test expect_num_outputs="1"> |
| 528 <!-- test map-hifi uncompressed reference--> | 528 <!-- test map-hifi uncompressed reference--> |
| 529 <param name="reference_source_selector" value="history" /> | 529 <param name="reference_source_selector" value="history" /> |
| 530 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa"/> | 530 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa"/> |
| 531 <param name="fastq_input_selector" value="single"/> | 531 <param name="fastq_input_selector" value="single"/> |
| 532 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/> | 532 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/> |
| 533 <param name="analysis_type_selector" value="map-hifi"/> | 533 <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" /> | 534 <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-2-fasta.bam" lines_diff="4" /> |
| 535 </test> | 535 </test> |
| 536 <test> | 536 <test expect_num_outputs="1"> |
| 537 <!-- test kmer ocurrence interval option --> | 537 <!-- test kmer ocurrence interval option --> |
| 538 <param name="reference_source_selector" value="history" /> | 538 <param name="reference_source_selector" value="history" /> |
| 539 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> | 539 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
| 540 <param name="fastq_input_selector" value="single"/> | 540 <param name="fastq_input_selector" value="single"/> |
| 541 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> | 541 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> |