Mercurial > repos > iuc > minimap2
comparison minimap2.xml @ 15:7db8d4bc1eea draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 166f7df2fa4bbcdb5c4c66a55185d5d595902ac9"
| author | iuc |
|---|---|
| date | Fri, 08 Oct 2021 09:48:01 +0000 |
| parents | 09b53c1d4ab1 |
| children | c0c2d0941de8 |
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| 14:09b53c1d4ab1 | 15:7db8d4bc1eea |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="minimap2" name="Map with minimap2" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" 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> | |
| 4 <macros> | 7 <macros> |
| 5 <import>macros.xml</import> | 8 <import>macros.xml</import> |
| 6 </macros> | 9 </macros> |
| 7 <expand macro="edam_ontology"/> | 10 <expand macro="edam_ontology"/> |
| 8 <expand macro="requirements"/> | 11 <expand macro="requirements"/> |
| 382 </action> | 385 </action> |
| 383 </when> | 386 </when> |
| 384 </conditional> | 387 </conditional> |
| 385 </actions> | 388 </actions> |
| 386 <change_format> | 389 <change_format> |
| 387 <when input="io_options.output_format" value="paf" format="tabular" /> | 390 <when input="io_options.output_format" value="paf" format="paf" /> |
| 388 <when input="io_options.output_format" value="CRAM" format="cram" /> | 391 <when input="io_options.output_format" value="CRAM" format="cram" /> |
| 389 </change_format> | 392 </change_format> |
| 390 </data> | 393 </data> |
| 391 </outputs> | 394 </outputs> |
| 392 <tests> | 395 <tests> |
| 483 <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" /> | 486 <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" /> |
| 484 <param name="fastq_input_selector" value="single"/> | 487 <param name="fastq_input_selector" value="single"/> |
| 485 <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" /> | 488 <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" /> |
| 486 <param name="analysis_type_selector" value="ava-ont"/> | 489 <param name="analysis_type_selector" value="ava-ont"/> |
| 487 <param name="output_format" value="paf"/> | 490 <param name="output_format" value="paf"/> |
| 488 <output name="alignment_output" ftype="tabular" file="mini_reads.paf" /> | 491 <output name="alignment_output" ftype="paf" file="mini_reads.paf" /> |
| 489 </test> | 492 </test> |
| 490 <test> | 493 <test> |
| 491 <!-- test self-homology mode --> | 494 <!-- test self-homology mode --> |
| 492 <param name="reference_source_selector" value="history" /> | 495 <param name="reference_source_selector" value="history" /> |
| 493 <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" /> | 496 <param name="ref_file" ftype="fasta" value="minimap2-self-homology.fasta" /> |
| 514 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa.gz"/> | 517 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa.gz"/> |
| 515 <param name="fastq_input_selector" value="single"/> | 518 <param name="fastq_input_selector" value="single"/> |
| 516 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/> | 519 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/> |
| 517 <param name="analysis_type_selector" value="map-hifi"/> | 520 <param name="analysis_type_selector" value="map-hifi"/> |
| 518 <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" /> | 521 <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-fasta.bam" lines_diff="4" /> |
| 522 </test> | |
| 523 <test> | |
| 524 <!-- test map-hifi uncompressed reference--> | |
| 525 <param name="reference_source_selector" value="history" /> | |
| 526 <param name="ref_file" ftype="fasta" value="pacbio_hifi_assembly.fa"/> | |
| 527 <param name="fastq_input_selector" value="single"/> | |
| 528 <param name="fastq_input1" ftype="fastqsanger" value="pacbio_hifi_reads.fasta.gz"/> | |
| 529 <param name="analysis_type_selector" value="map-hifi"/> | |
| 530 <output name="alignment_output" ftype="bam" file="minimap2-test_hifi-2-fasta.bam" lines_diff="4" /> | |
| 519 </test> | 531 </test> |
| 520 <test> | 532 <test> |
| 521 <!-- test kmer ocurrence interval option --> | 533 <!-- test kmer ocurrence interval option --> |
| 522 <param name="reference_source_selector" value="history" /> | 534 <param name="reference_source_selector" value="history" /> |
| 523 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> | 535 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |